| 1 |
gnomAD (Genome Aggregation Database)https://gnomad.broadinstitute.org/ |
Catalogues different types of variation and their potential functional impact. It aggregates exome and genome sequencing data from a variety of large-scale sequencing projects. Systematically incorporates information about exon expression into the interpretation of variants. Its transcript-level annotation metric known as the ‘proportion expressed across transcripts’, quantifies isoform expression for variants. The latest version released in November 2023, includes data from 807,162 total individuals | Karczewski KJ, Francioli LC, et al., Genome Aggregation Database Consortium; The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020 May;581(7809):434-443. doi: 10.1038/s41586-020-2308-7. Epub 2020 May 27. PMID: 32461654; PMCID: PMC7334197.
| 2020 | 50 |
Online |
| 2 |
1000 Genomeshttp://www.1000genomes.org |
1) Provides information on the validated haplotype map of 38 million single nucleotide polymorphisms, 1.4 million short insertions and deletions, and more than 14,000 larger deletions. 2) It aims to provide an accurate and better localization of disease associated variants in GWAS. | 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012 Nov 1;491(7422):56-65. doi: 10.1038/nature11632. PubMed PMID: 23128226; PubMed Central PMCID: PMC3498066
| 2012 | 62 |
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| 3 |
HapMaphttp://hapmap.ncbi.nlm.nih.gov/ |
Identifies and catalogs genetic similarities and differences in human beings and compares the genetic sequences of different individuals to find chromosomal regions where genetic variants are shared | International HapMap Consortium. The International HapMap Project. Nature. 2003 Dec 18;426(6968):789-96. PubMed PMID: 14685227.
| 2003 | 70 |
Online. The resource got retired in 2016 and the archived data is available via FTP
NCBI has retired the HapMap resource as on June 16, 2016 but the archived HapMap data will continue to be available via FTP from ftp://ftp.ncbi.nlm.nih.gov/hapmap/. |
| 4 |
Haploviewwww.broad.mit.edu/mpg/haploview/ |
1) Provides computation of linkage disequilibrium statistics and population haplotype patterns from primary genotype data. 2) Uses genotypic file (.ped file & .info file) as input and performs LD plots for highly associated markers and other statistics for it; also provides haplotype blocks for highly associated markers and performs other complex statistics for it (association tests for the SNP markers). 3) Mainly a useful tool for visualizing Hapmap data. | Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics. 2005 Jan 15;21(2):263-5. Epub 2004 Aug 5. PubMed PMID: 15297300.
| 2005 | 71 |
Freely downloadable |
| 5 |
dbSNPhttp://www.ncbi.nlm.nih.gov/projects/SNP/ |
A central repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms. | Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PubMed PMID: 11125122.
| 2001 | 74 |
Online |
| 6 |
SIFT - Sorting Tolerant From Intoleranthttp://sift.jcvi.org/ |
1) Restrict to coding variants -input- chromosome coordinates, orientation (1,-1) and alleles divides the variants into coding & non-coding variants. 2) SIFT nonsynonymous single nucleotide variants (genome-scale)-input-chromosome coordinates, orientation (1,-1) and alleles shows where in genome region(genic & non genic region) they are present & also OMIM ID associated with that variant. 3) Classify coding indels (Insertion / Deletion polymorphisms)-input-chromosome coordinates, orientation (1,-1) and indels- filters them out to coding indels. 4)SIFT dbSNP-input- list of rs-ids having impact on protein function or not (tolerating/damaging) from NCBI's dbSNP (build 132) database. | Ng PC, Henikoff S. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003 Jul 1;31(13):3812-4. PubMed PMID: 12824425.
| 2003 | 81 |
URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 7 |
SNPs&GOhttp://snps-and-go.biocomp.unibo.it/snps-and-go/ |
1) Prediction tool freely available. 2) Predicts the mutation that are likely to be related in the insurgence of diseases in human. | Calabrese R, Capriotti E, Fariselli P, Martelli PL, Casadio R. Functional annotations improve the predictive score of human disease-related mutations in proteins. Hum Mutat. 2009 Aug 1;30(8):1237-44. PubMed PMID: 19514061
| 2009 | 82 |
Online |
| 8 |
DnaSPhttp://www.ub.edu/dnasp |
1) Analysis on multiple data files. 2) Haplotype phasing. 3) Analysis of insertion/deletion polymorphism data. 4) Visualizes sliding window results integration with available genome annotations in the UCSC browser. | Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009 Jun 1;25(11):1451-2. Epub 2009 Apr 3. PubMed PMID: 19346325.
| 2009 | 83 |
Freely downloadable |
| 9 |
ClinVarhttps://www.ncbi.nlm.nih.gov/clinvar/ |
Reports data about relationships between human variations and phenotypes, with supporting evidence. The database includes germline and somatic variants of any size, type or genomic location. It mainly aggregates information about genomic variation and its relationship to human health. | Landrum MJ, Lee JM, Benson M, Brown G, Chao C, Chitipiralla S, Gu B, Hart J, Hoffman D, Hoover J, Jang W, Katz K, Ovetsky M, Riley G, Sethi A, Tully R, Villamarin-Salomon R, Rubinstein W, Maglott DR. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res. 2016 Jan 4;44(D1):D862-8. doi: 10.1093/nar/gkv1222. Epub 2015 Nov 17. PMID: 26582918; PMCID: PMC4702865.
| 2016 | 83 |
Online |
| 10 |
DataBiNS-Viz |
A visualization and exploration environment for non-synonymous coding single nucleotide polymorphisms (nsSNPs) data. | Fong CC, Edward AK, Mark DW, Scott JT (2008). DataBiNS-Viz: A Web-Based Tool for Visualization of Non-Synonymous SNP Data. J Proteomics Bioinform 1: 233-236. doi:10.4172/jpb.1000029
| Not available | 84 |
- |
| 11 |
QSNPlite |
Assists in the quantitative characterization of SNPs and estimates their allele frequencies. | Tahira T, Okazaki Y, Miura K, Yoshinaga A, Masumoto K, Higasa K, Kukita Y, Hayashi K. QSNPlite, a software system for quantitative analysis of SNPs based on capillary array SSCP analysis. Electrophoresis. 2006 Oct;27(19):3869-78. PubMed PMID: 16960832
| 2006 | 84 |
Program runs on Windows XP. Can be obtained from Kenshi Hayashi by sending e-mail to khayashi@gen.kyushu-u.ac.jp |
| 12 |
HapMap SNP Scanner |
Provides information on novel SNPs, which are responsible for minor H (minor histocompatibility) antigens generation. | Yamamura T, Hikita J, Bleakley M, Hirosawa T, Sato-Otsubo A, Torikai H, Hamajima T, Nannya Y, Demachi-Okamura A, Maruya E, Saji H, Yamamoto Y, Takahashi T, Emi N, Morishima Y, Kodera Y, Kuzushima K, Riddell SR, Ogawa S, Akatsuka Y. HapMap SNP Scanner: an online program to mine SNPs responsible for cell phenotype. Tissue Antigens. 2012 Aug;80(2):119-25. doi: 10.1111/j.1399-0039.2012.01883.x. Epub 2012 May 8. PubMed PMID: 22568758; PubMed Central PMCID: PMC3635041
| 2012 | 84 |
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| 13 |
OMIMhttps://www.omim.org/ |
Lists the human genes and genetic phenotypes, which focuses on the relationship between phenotype and genotype. Provides information on all known mendelian disorders and over 16,000 genes. It is updated daily, and the entries contain copious links to other genetics resources. | Hamosh A, Scott AF, Amberger J, Bocchini C, Valle D, McKusick VA. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 2002 Jan 1;30(1):52-5. doi: 10.1093/nar/30.1.52. PMID: 11752252; PMCID: PMC99152.
| 2002 | 87 |
Online |
| 14 |
GCTAhttp://gump.qimr.edu.au/gcta/ |
Analysis of the proportion of phenotypic variance based on the genome/chromosome-wide SNPs for complex traits. 1) Finds the genetic relationship from genome-wide SNPs. 2) Calculates the variance explained by all the autosomal SNPs. 3) Finds the genetic variance associated with the X-chromosome. 4) Estimates the LD structure encompassing a list of target SNPs. | Yang J, Lee SH, Goddard ME, Visscher PM. GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet. 2011 Jan 7;88(1):76-82. Epub 2010 Dec 17. PubMed PMID: 21167468.
| 2011 | 88 |
Freely downloadable. URL not working as on 2023. |
| 15 |
GENOMEhttp://www.sph.umich.edu/csg/liang/genome/ |
| Liang L, Zollner S, Abecasis GR. GENOME: a rapid coalescent-based whole genome simulator. Bioinformatics. 2007 Jun 15;23(12):1565-7. Epub 2007 Apr 25. PubMed PMID: 17459963.
| 2007 | 90 |
Freely downloadable. URL not working as on 30 Nov 2013 (confirmed in 2017 and 2023) |
| 16 |
F-SNPhttp://compbio.cs.queensu.ca/F-SNP/ |
Provides integrated information about the functional effects of SNPs mainly in terms of disease association studies. | Lee PH, Shatkay H. F-SNP: computationally predicted functional SNPs for disease association studies. Nucleic Acids Res. 2008 Jan;36(Database issue):D820-4. Epub 2007 Nov 5. PubMed PMID: 17986460.
| 2008 | 90 |
Online. URL not working (as on 31 Aug 2016); confirmed in Feb 2017 and Dec 2023 |
| 17 |
G-SNPM http://www.interomics.eu/sp1-wp2. |
Maps a short sequence representative of a SNP against a reference DNA sequence and provides information on the physical position of the SNP in that sequence. | Manconi A, Orro A, Manca E, Armano G, Milanesi L. A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units. BMC Bioinformatics. 2014;15 Suppl 1:S10. doi: 10.1186/1471-2105-15-S1-S10. Epub 2014 Jan 10. PubMed PMID: 24564714; PubMed Central PMCID: PMC4015528.
| 2014 | 90 |
URL not working as on 10 Jan 2015; confirmed in Dec 2023 |
| 18 |
PolyPhenhttp://genetics.bwh.harvard.edu/pph/ |
Predicts the impact of an amino acid substitution on the structure and function of a human protein. | Ramensky V, Bork P, Sunyaev S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res. 2002 Sep 1;30(17):3894-900. PubMed PMID: 12202775.
| 2002 | 91 |
Online.URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 19 |
F-nsSNP-Syn-Genhttp://sites.google.com/site/compgensite/f-nssnp-syn-gen |
Information on experimentally validated functional nsSNPs in human synaptic genes. | | Not available | 92 |
URL not working as on Dec 2023 |
| 20 |
SNP-Flankplushttp://bio.kuas.edu.tw/snp-flankplus/ |
Retrieves SNP flanking sequences from the dbSNP and nucleotide databases of NCBI, which can be useful to design PCR primers for the SNP genotyping methods. | Yang CH, Cheng YH, Chuang LY, Chang HW. SNP-Flankplus: SNP ID-centric retrieval for SNP flanking sequences. Bioinformation. 2008;3(4):147-9. Epub 2008 Dec 6. PubMed PMID: 19238236.
| 2008 | 92 |
Online. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 21 |
SNP-o-matichttp://snpomatic.sourceforge.net/ |
Provides a list of found known SNPs (either reference or alternate allele) while analyzing Solexa reads and comparing them to a reference so, it serves as a Solexa-based genotyping application. | Manske HM, Kwiatkowski DP. SNP-o-matic. Bioinformatics. 2009 Sep 15;25(18):2434-5. Epub 2009 Jul 2. PubMed PMID: 19574284.
| 2009 | 92 |
Freely downloadable |
| 22 |
SNP-VISTAhttp://genome.lbl.gov/vista/snpvista |
Serves as a visualization tool. It provides: 1) mapping of SNPs to gene structure; 2) classification of SNPs, based on their location in the gene, frequency of occurrence in samples and allele composition; 3) clustering is done based on user-defined subsets of SNPs, highlighting haplotypes as well as recombinant sequences. | Shah N, Teplitsky MV, Minovitsky S, Pennacchio LA, Hugenholtz P, Hamann B, Dubchak IL. SNP-VISTA: an interactive SNP visualization tool. BMC Bioinformatics. 2005 Dec 8;6:292. PubMed PMID: 16336665.
| 2005 | 92 |
Online & freely downloadable |
| 23 |
SOAP2 (Short Oligonucleotide Analysis Package)http://soap.genomics.org.cn/ |
Provides a feature of SNP detection from alignment of short reads on a reference genome. | Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 2009 Aug 1;25(15):1966-7. Epub 2009 Jun 3. PubMed PMID: 19497933.
| 2009 | 92 |
Freely downloadable |
| 24 |
Structurehttp://pritch.bsd.uchicago.edu/structure.html |
A software package, which is used to investigate population structure. It can be applied to most of the commonly-used genetic markers, including SNPs, microsatellites, RFLPs and AFLPs. | | Not available | 92 |
Freely downloadable |
| 25 |
HMDB - Human Metabolome Databasehttp://www.hmdb.ca/ |
1) Contains detailed information about small molecule metabolites found in the human body. 2) The SNP data field (found in HMDB's Enzyme section) is displayed in the form of hyperlinked summary tables, which contains information on their type (synonymous, nonsynonymous), location, validation status and population distributions. | Wishart DS, Tzur D, Knox C, Eisner R, Guo AC, Young N, Cheng D, Jewell K, Arndt D, Sawhney S, Fung C, Nikolai L, Lewis M, Coutouly MA, Forsythe I, Tang P, Shrivastava S, Jeroncic K, Stothard P, Amegbey G, Block D, Hau DD, Wagner J, Miniaci J, Clements M, Gebremedhin M, Guo N, Zhang Y, Duggan GE, Macinnis GD, Weljie AM, Dowlatabadi R, Bamforth F, Clive D, Greiner R, Li L, Marrie T, Sykes BD, Vogel HJ, Querengesser L. HMDB: the Human Metabolome Database. Nucleic Acids Res. 2007 Jan;35(Database issue):D521-6. PubMed PMID: 17202168.
| 2007 | 94 |
Online |
| 26 |
RegulomeDBhttp://regulomedb.org/ |
1) Annotates as well as prioritizes potential regulatory variants from the human genome. 2) It is an online composite database as well as a prediction tool, generating a score and assessing the evidence for regulatory potential. | Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, Karczewski KJ, Park J, Hitz BC, Weng S, Cherry JM. Annotation of functional variation in personal genomes using RegulomeDB. Genome research. 2012 Sep 1;22(9):1790-7. PubMed PMID: 22955989
| 2012 | 94 |
Online |
| 27 |
SNPStatshttp://bioinfo.iconcologia.net/snpstats/start.htm |
Performs analysis of multiple SNPs: haplotype frequency estimation, analysis of association of haplotypes with the response, including analysis of interactions. | Sole X, Guino E, Valls J, Iniesta R, Moreno V. SNPStats: a web tool for the analysis of association studies. Bioinformatics. 2006 Aug 1;22(15):1928-9. Epub 2006 May 23. PubMed PMID: 16720584.
| 2006 | 95 |
Online. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 28 |
Drug-SNPhttp://ns.nihcgc.re.kr/ ljy75/Drug-SNP.html |
1) Provides information about SNPs present within genes, which code for drug targets. 2) Provides combined information on drug target proteins (including enzyme, receptor, and agonists/antagonists), genes and SNPs. | | Not available | 96 |
URL not working as on 30 Nov 2013 (confirmed in 2017 and 2023) |
| 29 |
MAP-O-MAThttp://compgen.rutgers.edu/mapomat/ |
Provides automated linkage mapping of human polymorphic DNA markers. | Kong X, Matise TC. MAP-O-MAT: internet-based linkage mapping. Bioinformatics. 2005 Feb 15;21(4):557-9. Epub 2004 Sep 16. PMID:15374870
| 2005 | 96 |
Online. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 30 |
Seq-SNPinghttp://bio.kuas.edu.tw/Seq-SNPing |
A sequence alignment program, which incorporates SNP identification tools for association studies. | Chang HW, Chuang LY, Cheng YH, Ho CH, Wen CH, Yang CH. Seq-SNPing: multiple-alignment tool for SNP discovery, SNP ID identification, and RFLP genotyping. OMICS. 2009 Jun;13(3):253-60. PubMed PMID: 19514837.
| 2009 | 96 |
It requires the Java Running Environment (JRE 1.5.0) to run properly. URL not working (as on Dec 2023) |
| 31 |
Synthesis-Viewhttp://chgr.mc.vanderbilt.edu/ritchielab/method.php?method=synthesisview |
A visualization tool, which plots information on SNP genomic locations, presence of the SNP in a specific study or analysis, as well as related data such as genetic effect size and summary phenotype information, according to user preferences. | Pendergrass SA, Dudek SM, Crawford DC, Ritchie MD. Synthesis-View: visualization and interpretation of SNP association results for multi-cohort, multi-phenotype data and meta-analysis. BioData Min. 2010 Dec 16;3:10. PubMed PMID: 21162740.
| 2010 | 96 |
Online. URL not working (as on 30 Aug 2016); confirmed in Feb 2017 and Dec 2023 |
| 32 |
adegenet 1.3-1 http://adegenet.r-forge.r-project.org/ |
Performs efficient genome-wise SNP data handling and analysis, visualization of SNPs density and test for the randomness of their distribution. | Jombart T, Ahmed I. adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics. 2011 Nov 1;27(21):3070-1. doi: 10.1093/bioinformatics/btr521. Epub 2011 Sep 16. PubMed PMID: 21926124; PubMed Central PMCID: PMC3198581.
| 2011 | 96 |
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| 33 |
SeattleSeq Annotationhttp://snp.gs.washington.edu/SeattleSeqAnnotation141/index.jsp |
Provides annotation (including dbSNP rs IDs, gene names and accession numbers, variation functions) of SNVs (single-nucleotide variations) and small indels, both known and novel. | Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, Shaffer T, Wong M, Bhattacharjee A, Eichler EE, Bamshad M. Targeted capture and massively parallel sequencing of 12 human exomes. Nature. 2009 Sep 10;461(7261):272-6. PubMed PMID: 19684571
| 2009 | 96 |
Online. URL not working (as on 19 Feb 2017); confirmed in Dec 2023 |
| 34 |
BioMarthttp://www.biomart.org/ |
Applicable in solving biological use cases such as SNP selection for candidate gene screening or annotation of microarray results. | Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A. BioMart--biological queries made easy. BMC Genomics. 2009 Jan 14;10:22. PubMed PMID: 19144180.
| 2009 | 97 |
Online. URL not working (as on Dec 2023) |
| 35 |
LocusZoomhttp://csg.sph.umich.edu/locuszoom/ |
Plots regional association results from genome-wide association scans or candidate gene studies. | Pruim RJ, Welch RP, Sanna S, Teslovich TM, Chines PS, Gliedt TP, Boehnke M, Abecasis GR, Willer CJ. LocusZoom: regional visualization of genome-wide association scan results. Bioinformatics. 2010 Sep 15;26(18):2336-7. Epub 2010 Jul 15. PMID:20634204
| 2010 | 97 |
Online |
| 36 |
SNPinfohttp://snpinfo.niehs.nih.gov/ |
| Xu Z, Taylor JA. SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies. Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W600-5. Epub 2009 May 5. PubMed PMID: 19417063.
| 2009 | 97 |
Freely downloadable |
| 37 |
SNPSpD - SNP SPectral Decompositionhttp://gump.qimr.edu.au/general/daleN/SNPSpD/ |
Based on spectral decomposition, it provides a correlation between SNPs and linkage disequilibrium.. | Nyholt DR. A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequilibrium with each other. Am J Hum Genet. 2004 Apr;74(4):765-9. Epub 2004 Mar 2. PubMed PMID: 14997420.
| 2004 | 97 |
Downloadable. URL not working as on 12 Dec 2023 |
| 38 |
Varsomehttps://varsome.com/ |
It is a powerful variant search engine, sharing global expertise on human variants. It features a robust aggregated knowledge base consisting of over 140 cross-referenced data resource. VarSome.com is a search engine, aggregator and impact analysis tool for human genetic variation and a community-driven project aiming at sharing global expertise on human variants. | Christos Kopanos, Vasilis Tsiolkas, Alexandros Kouris, Charles E Chapple, Monica Albarca Aguilera, Richard Meyer, Andreas Massouras, VarSome: the human genomic variant search engine, Bioinformatics, Volume 35, Issue 11, June 2019, Pages 1978–1980, https://doi.org/10.1093/bioinformatics/bty897
| 2019 | 97 |
Online |
| 39 |
CNAReporternot available |
| Kotliarov Y, Bozdag S, Cheng H, Wuchty S, Zenklusen JC, Fine HA. CNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations. BMC Med Genomics. 2010 Apr 9;3:11. PubMed PMID: 20380730.
| 2010 | 98 |
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| 40 |
GenoA - Genome AnalyzerNOT AVAILABLE |
A data mining and visualization tool, which extracts exons and SNPs from mammalian genomic sequences. | Liu Y, Wang Y, Folander K, Xie G, Blevins R. An interactive tool for extracting exons and SNP from genomic sequence: isolation of HCN1 and HCN3 ion channel genes. J Bioinform Comput Biol. 2003 Oct;1(3):433-46. PubMed PMID: 15290763.
| 2003 | 98 |
- |
| 41 |
GOLD - Graphical Overview of Linkage Disequilibriumhttp://www.well.ox.ac.uk/asthma/GOLD |
| Abecasis GR, Cookson WO. GOLD--graphical overview of linkage disequilibrium. Bioinformatics. 2000 Feb;16(2):182-3. PubMed PMID: 10842743.
| 2000 | 98 |
URL not working as on 30 Nov 2013 (confirmed in 2017 and 2023) |
| 42 |
HEPTAPLEX SNPNOT AVAILABLE |
Provides allele frequency data of the South-West Poland population. | | Not available | 98 |
- |
| 43 |
LD-Plushttps://chgr.mc.vanderbilt.edu/ldplus/create/setparams |
1) It is a visualization tool for display of single SNP statistics in the context of linkage disequilibrium and haplotype structures. 2) It also displays continuous and categorical SNP statistics. 3) It parses Haploview output to display both D' and r blocks, and haplotype frequencies. LD-Plus can display both continuous and categorical SNP statistics, and r2 LD plots. | Bush WS, Dudek SM, Ritchie MD. Visualizing SNP statistics in the context of linkage disequilibrium using LD-Plus. Bioinformatics. 2010 Feb 15;26(4):578-9. Epub 2010 Feb 3. PMID:20130027
| 2010 | 98 |
Online. URL not working as on Feb 2017 and confirmed in Dec 2023. |
| 44 |
SimHap GUInot available |
An integrated graphical analysis tool for conducting epidemiological, single SNP and haplotype-based association analysis. | Carter KW, McCaskie PA, Palmer LJ. SimHap GUI: an intuitive graphical user interface for genetic association analysis. BMC Bioinformatics. 2008 Dec 25;9:557. PubMed PMID: 19109877.
| 2008 | 98 |
Online |
| 45 |
Snap - Single Nucleotide Polymorphism Annotation Platformhttp://snap.genomics.org.cn/ |
1)Performs detailed analysis of human genes and their variations. The input can be-gene name, chromosome location, marker position, clone & SNP rs ids. 2)Provides a gene-gene relationship network on protein-protein interaction data, metabolic pathway connections and phylogenetic relations. 3) Assits in primer designing for amplification/seqeuncing of cDNA, genomic DNA, introns or exons. 4) Information on SNPs affecting RNA splicing, types of SNPs (synonymus, non-synonymus & in-dels), regions where SNP is present in the gene/genome region. | Li S, Ma L, Li H, Vang S, Hu Y, Bolund L, Wang J. Snap: an integrated SNP annotation platform. Nucleic Acids Res. 2007 Jan;35(Database issue):D707-10. Epub 2006 Nov 29. PubMed PMID: 17135198.
| 2007 | 98 |
Program files available for download. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 46 |
SNPitnot available |
Provides functional annotation information on SNPs, which is important in understanding the genome-wide association studies. | Shen TH, Carlson CS, Tarczy-Hornoch P. SNPit: a federated data integration system for the purpose of functional SNP annotation. Comput Methods Programs Biomed. 2009 Aug;95(2):181-9. Epub 2009 Mar 26. PubMed PMID: 19327864.
| 2009 | 98 |
Online |
| 47 |
SNPositionNOT AVAILABLE |
| | Not available | 98 |
Freely downloadable |
| 48 |
SNPpyNOT AVAILABLE |
| | Not available | 98 |
- |
| 49 |
WormBasehttp://www.wormbase.org/ |
Contains over 10,000 alleles with molecular information, which facilitates the structure/function studies and sequencing data in the polymorphic strains, has identified over 1,70,000 single nucleotide polymorphisms. | Harris TW, Antoshechkin I, Bieri T, Blasiar D, Chan J, Chen WJ, De La Cruz N, Davis P, Duesbury M, Fang R, Fernandes J, Han M, Kishore R, Lee R, Müller HM, Nakamura C, Ozersky P, Petcherski A, Rangarajan A, Rogers A, Schindelman G, Schwarz EM, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Yook K, Durbin R, Stein LD, Spieth J, Sternberg PW. WormBase: a comprehensive resource for nematode research. Nucleic Acids Res. 2010 Jan;38(Database issue):D463-7. Epub 2009 Nov 12. PubMed PMID: 19910365
| 2010 | 98 |
Online |
| 50 |
A SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua)NOT AVAILABLE |
An extensive resource of SNP markers for Atlantic cod, Gadus morhua. | Hubert S, Higgins B, Borza T, Bowman S. Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua). BMC Genomics. 2010 Mar 22;11:191. PubMed PMID: 20307277
| 2010 | 98 |
- |
| 51 |
A SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei)NOT AVAILABLE |
Information on SNPs in Pacific white shrimp (Litopenaeus vannamei). | Ciobanu DC, Bastiaansen JW, Magrin J, Rocha JL, Jiang DH, Yu N, Geiger B, Deeb N, Rocha D, Gong H, Kinghorn BP, Plastow GS, van der Steen HA, Mileham AJ. A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei). Anim Genet. 2010 Feb;41(1):39-47. Epub 2009 Oct 2. PubMed PMID: 19799596.
| 2010 | 98 |
- |
| 52 |
GEAD & JG-SNPhttp://www.tmghig.jp/jg-snp/english/E_top.html |
Provides information on the role of genetic polymorphism (single nucleotide polymorphism) in the development of geriatric disease among the Japanese population. | Sawabe M, Arai T, Kasahara I, Esaki Y, Nakahara K, Hosoi T, Orimo H, Takubo K, Murayama S, Tanaka N; Tokyo Metropolitan Geriatric Medical Center; Japan Science and Technology Agency. Developments of geriatric autopsy database and Internet-based database of Japanese single nucleotide polymorphisms for geriatric research (JG-SNP). Mech Ageing Dev. 2004 Aug;125(8):547-52. PubMed PMID: 15336912.
| 2004 | 98 |
Online |
| 53 |
Genevarhttp://www.sanger.ac.uk/resources/software/genevar/ |
It is a platform of database and web services designed for data integration, analysis and visualization of SNP-gene associations in eQTL (expression quantitative trait loci) studies. | Yang TP, Beazley C, Montgomery SB, Dimas AS, Gutierrez-Arcelus M, Stranger BE, Deloukas P, Dermitzakis ET. Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies. Bioinformatics. 2010 Oct 1;26(19):2474-6. Epub 2010 Aug 10. PubMed PMID: 20702402.
| 2010 | 98 |
Freely downloadable. URL not working (as on 31 Aug 2016); confirmed in Feb 2017 and Dec 2023 |
| 54 |
Panzeahttp://www.panzea.org/ |
Finds polymorphism between two inbred lines of maize. | Zhao W, Canaran P, Jurkuta R, Fulton T, Glaubitz J, Buckler E, Doebley J, Gaut B, Goodman M, Holland J, Kresovich S, McMullen M, Stein L, Ware D. Panzea: a database and resource for molecular and functional diversity in the maize genome. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D752-7. PubMed PMID: 16381974.
| 2006 | 98 |
Online |
| 55 |
PhD-SNP - Predictor of human Deleterious Single Nucleotide Polymorphismshttp://gpcr2.biocomp.unibo.it/cgi/predictors/PhD-SNP/PhD-SNP.cgi |
Provides information on the mutant position present in the protein sequences to predict the deleterious SNPs. | Capriotti E, Calabrese R, Casadio R. Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinformatics. 2006 Nov 15;22(22):2729-34. Epub 2006 Aug 7. PubMed PMID: 16895930.
| 2006 | 98 |
Online. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 56 |
SCAN - SNP and Copy number Annotationhttp://www.scandb.org/newinterface/about.html |
Provides both physical and funtional annotation of SNPs. | Gamazon ER, Zhang W, Konkashbaev A, Duan S, Kistner EO, Nicolae DL, Dolan ME, Cox NJ. SCAN: SNP and copy number annotation. Bioinformatics. 2010 Jan 15;26(2):259-62. Epub 2009 Nov 17. PubMed PMID: 19933162
| 2010 | 98 |
Online. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 57 |
SNP resource for Pacific white shrimp (Litopenaeus vannamei)NOT AVAILABLE |
SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei) | Ciobanu DC, Bastiaansen JW, Magrin J, Rocha JL, Jiang DH, Yu N, Geiger B, Deeb N, Rocha D, Gong H, Kinghorn BP, Plastow GS, van der Steen HA, Mileham AJ. A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei). Anim Genet. 2010 Feb;41(1):39-47. Epub 2009 Oct 2. PubMed PMID: 19799596.
| 2010 | 98 |
- |
| 58 |
SNP Resource for Human Chromosome 22NOT AVAILABLE |
Reports the dentification and characterization of 12,267 potential variants (SNPs and other small insertions/deletions) of human chromosome 22. | Dawson E, Chen Y, Hunt S, Smink LJ, Hunt A, Rice K, Livingston S, Bumpstead S, Bruskiewich R, Sham P, Ganske R, Adams M, Kawasaki K, Shimizu N, Minoshima S, Roe B, Bentley D, Dunham I. A SNP resource for human chromosome 22: extracting dense clusters of SNPs from the genomic sequence. Genome Res. 2001 Jan;11(1):170-8. PubMed PMID: 11156626.
| 2001 | 98 |
- |
| 59 |
DIYABC v2.0http://www1.montpellier.inra.fr/CBGP/diyabc |
A software package, which allows the analysis of single nucleotide polymorphism data at large number of loci, apart from microsatellite and DNA sequence data. | Cornuet JM, Pudlo P, Veyssier J, Dehne-Garcia A, Gautier M, Leblois R, Marin JM, Estoup A. DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data. Bioinformatics. 2014 Jan 13. [Epub ahead of print] PubMed PMID: 24389659.
| 2014 | 98 |
URL not working (as on 12 Dec 2023) |
| 60 |
METU-SNPNot available |
A Java based integrated desktop application, which helps in the dentification of SNPs that are involved in the etiology of complex diseases. | Ustünkar G, Aydın Son Y. METU-SNP: an integrated software system for SNP-complex disease association analysis. J Integr Bioinform. 2011 Dec 12;8(1):187. doi: 10.2390/biecoll-jib-2011-187. PubMed PMID: 22156365.
| 2011 | 98 |
|
| 61 |
FunciSNPNot available |
It is a R/Bioconductor software package, which enables the identification of candidate functional SNPs by integrating information from tagSNP locations, lists of linked SNPs from the 1000 genomes project and locations of chromatin features which may have functional significance. | Coetzee SG, Rhie SK, Berman BP, Coetzee GA, Noushmehr H. FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs. Nucleic Acids Res. 2012 Oct;40(18):e139. doi: 10.1093/nar/gks542. Epub 2012 Jun 8. PubMed PMID: 22684628; PubMed Central PMCID: PMC3467035.
| 2012 | 98 |
|
| 62 |
SNPpyhttp://bitbucket.org/faheem/snppy |
Provides integrated management and manipulation of genotype and phenotype data from GWAS studies. | Mitha F, Herodotou H, Borisov N, Jiang C, Yoder J, Owzar K. SNPpy--database management for SNP data from genome wide association studies. PLoS One. 2011;6(10):e24982. doi: 10.1371/journal.pone.0024982. Epub 2011 Oct 19. PubMed PMID: 22039405; PubMed Central PMCID: PMC3198468
| 2011 | 98 |
URL not working (as on 19 Feb 2017); confirmed in Dec 2023 |
| 63 |
MutPred serverhttp://mutpred.mutdb.org/ |
Employed for the classification of an amino acid substitution (AAS) as either disease-associated or neutral | Li B, Krishnan VG, Mort ME, Xin F, Kamati KK, Cooper DN, Mooney SD, Radivojac P. Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinformatics. 2009 Nov 1;25(21):2744-50 PubMed PMID: 19734154
| 2009 | 98 |
Online |
| 64 |
dbNSFP-database for nonsynonymous SNPs functional predictionshttp://sites.google.com/site/jpopgen/dbNSFP |
1) Database for Human Non-synonymous SNPs. 2) Predicts nsSNPs function through compilation of four popular algorithms (SIFT, PolyPhen2, LRT and Mutantion Taster). | Liu X, Jian X, Boerwinkle E. dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. Human mutation. 2011 Aug 1;32(8):894-9. PubMed PMID: 21520341
| 2011 | 98 |
Downloadable |
| 65 |
ARTShttp://andromeda.gsf.de/arts |
An advanced tool for retrieval of SNPs in mouse. | Klaften M, Hrabé de Angelis M. ARTS: a web-based tool for the set-up of high-throughput genome-wide mapping panels for the SNP genotyping of mouse mutants. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W496-500. PubMed PMID: 15980520.
| 2005 | 99 |
Online (URL not working as on 26 October 2013), (confirmed in 2017 and 2023) |
| 66 |
Crossbowhttp://bowtie-bio.sourceforge.net/crossbow/index.shtml |
| Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL. Searching for SNPs with cloud computing. Genome Biol. 2009;10(11):R134. Epub 2009 Nov 20. PubMed PMID: 19930550.
| 2009 | 99 |
Online |
| 67 |
ECR browserhttp://ecrbrowser.dcode.org/ |
Visualizes and analyzes Evolutionary Conserved Regions (ECRs) in genomes of sequenced species and provides annotation of different genomic features, such as known genes, gene predictions, repetitive elements and single nucleotide polymorphisms. | Ovcharenko I, Nobrega MA, Loots GG, Stubbs L. ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W280-6. PubMed PMID: 15215395.
| 2004 | 99 |
Online |
| 68 |
FASTSNP- Function analysis and selection tool for single nucleotide polymorphismshttp://fastsnp.ibms.sinica.edu.tw/pages/input_CandidateGeneSearch.jsp |
Identifies and prioritizes high-risk SNPs according to their phenotypic risks and putative functional effects. A unique feature is that the functional effect information used for SNP prioritization is extracted from 11 external web servers at query time using a team of web wrapper agents, which keeps the data up-to- date. | Yuan HY, Chiou JJ, Tseng WH, Liu CH, Liu CK, Lin YJ, Wang HH, Yao A, Chen YT, Hsu CN. FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W635-41. PubMed PMID: 16845089.
| 2006 | 99 |
Online. URL not working as on Dec 2023 |
| 69 |
Pathhttp://genapha.icapture.ubc.ca/PathTutorial/ |
Provides information on SNPs and genetic association studies, which are collected from different online resources. | Zamar D, Tripp B, Ellis G, Daley D. Path: a tool to facilitate pathway-based genetic association analysis. Bioinformatics. 2009 Sep 15;25(18):2444-6. Epub 2009 Jul 23. PubMed PMID: 19628508.
| 2009 | 99 |
Freely downloadable. URL not working, shows server error (as on Dec 2023).
Freely downloadable |
| 70 |
PGA - Power for Genetic Association analyseshttp://dceg.cancer.gov/bb/tools/pga |
A package of algorithms and graphical user interfaces developed in Matlab for power and sample size calculation under various genetic models and statistical constraints. | Menashe I, Rosenberg PS, Chen BE. PGA: power calculator for case-control genetic association analyses. BMC Genet. 2008 May 13;9:36. PubMed PMID: 18477402.
| 2008 | 99 |
The website states that users without Matlab software should install first the MATLAB Component Runtime (MCR) on their computers. URL not working as on Dec 2023 |
| 71 |
PMUThttp://mmb2.pcb.ub.es:8080/PMut/ |
Provides fast and accurate prediction of single point amino acid mutations (which have a pathological character) by the use of neural networks. | Ferrer-Costa C, Gelpí JL, Zamakola L, Parraga I, de la Cruz X, Orozco M. PMUT: a web-based tool for the annotation of pathological mutations on proteins. Bioinformatics. 2005 Jul 15;21(14):3176-8. Epub 2005 May 6. PubMed PMID: 15879453.
| 2005 | 99 |
Online. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 72 |
POPTREE2http://www.kms.ac.jp/~genomelb/takezaki/poptree2 |
Constructs phylogenetic trees from allele frequency data and also measures genetic variation in a population and genetic differentiation among subdivided populations. | Takezaki N, Nei M, Tamura K. POPTREE2: Software for constructing population trees from allele frequency data and computing other population statistics with Windows interface. Mol Biol Evol. 2010 Apr;27(4):747-52. Epub 2009 Dec 18. PubMed PMID: 20022889.
| 2010 | 99 |
Installation required. |
| 73 |
PupaSuitehttp://pupasuite.bioinfo.cipf.es/ |
Provides information on SNPs within a gene along with additional data for the SNP like- validation status, type, frequency/population data and putative functional properties (pathological SNPs, SNPs disrupting potential transcription factor binding sites, intron/exon boundaries), information about LD parameters (based on genotype data from HapMap) and identifies haplotype blocks and tag SNPs. | Conde L, Vaquerizas JM, Dopazo H, Arbiza L, Reumers J, Rousseau F, Schymkowitz J, Dopazo J. PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W621-5. PubMed PMID: 16845085.
| 2006 | 99 |
Online registration |
| 74 |
Quake http://www.cbcb.umd.edu/software/quake |
A program to detect and correct errors in DNA sequencing reads and helps users to demonstrate significant improvements in de novo assembly and SNP detection. | Kelley DR, Schatz MC, Salzberg SL. Quake: quality-aware detection and correction of sequencing errors. Genome Biol. 2010;11(11):R116. Epub 2010 Nov 29. PubMed PMID: 21114842.
| 2010 | 99 |
Freely downloadable. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 75 |
SNAP - Screening for non-acceptable polymorphismshttp://www.rostlab.org/services/SNAP |
Evaluates the effects of single amino acid substitutions on protein function. | Bromberg Y, Rost B. SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res. 2007;35(11):3823-35. Epub 2007 May 25. PubMed PMID: 17526529.
| 2007 | 99 |
Online. It returns its results to the user via e-mail. |
| 76 |
SNPs3Dhttp://www.snps3d.org/ |
Asssigns functional effects of non-synonymous SNPs based on structure and sequence analysis. | Yue P, Melamud E, Moult J. SNPs3D: candidate gene and SNP selection for association studies. BMC Bioinformatics. 2006 Mar 22;7:166. PubMed PMID: 16551372.
| 2006 | 99 |
Online |
| 77 |
SPOT - SNP prioritization online toolhttps://spot.cgsmd.isi.edu/submit.php |
| Saccone SF, Bolze R, Thomas P, Quan J, Mehta G, Deelman E, Tischfield JA, Rice JP. SPOT: a web-based tool for using biological databases to prioritize SNPs after a genome-wide association study. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W201-9. Epub 2010 Jun 6. PubMed PMID: 20529875.
| 2010 | 99 |
Online. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 78 |
ProbABELhttp://www.genabel.org/manuals/ProbABEL |
Uses statistical approach to relate SNP information with genome-wide association studies. | Aulchenko YS, Struchalin MV, van Duijn CM. ProbABEL package for genome-wide association analysis of imputed data. BMC Bioinformatics. 2010 Mar 16;11:134. PubMed PMID: 20233392.
| 2010 | 99 |
Files for execution available. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 79 |
SNPnexushttp://www.snp-nexus.org/ |
It’s a SNP annotation tool, which helps in the selection of functionally relevant SNPs for large-scale genotyping studies. Allows single queries using dbSNP identifiers or chromosomal regions for annotating the known variants. | Chelala C, Khan A, Lemoine NR. SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms. Bioinformatics. 2009 Mar 1;25(5):655-61. Epub 2008 Dec 19. PubMed PMID: 19098027.
| 2009 | 99 |
Online |
| 80 |
PredictSNPhttp://loschmidt.chemi.muni.cz/predictsnp/ |
1) Predicts the disease-related mutations by the analysis of single nucleotide variants in the coding regions and the effect of amino acid substitution. 2) Serves as a consensus classifier, which combines six of the top performing tools for the prediction of the effects of mutation on protein function and the obtained results are provided together with the annotations extracted from the Protein Mutant Database and the UniProt database. | Bendl J, Stourac J, Salanda O, Pavelka A, Wieben ED, Zendulka J, Brezovsky J and Damborsky J. PredictSNP: Robust and accurate consensus classifier for prediction of disease-related mutations. PLoS Comput Bi7ol. 2014 Jan; 10(1):e1003440. doi: 10.1371/journal.pcbi.1003440. Epub 2014 Jan 16. PubMed PMID: 24453961; PMCID: PMC3894168.
| 2014 | 99 |
Tool contributed to the portal by Jarsolav Bendl (one of the developers of the tool) on May 14, 2014 |
| 81 |
kSNP v2https://sourceforge.net/projects/ksnp |
1) Finds SNPs and builds phylogenies for bacterial and viral genomes. 2) SNP discovery is based on k-mer analysis, and does not require multiple sequence alignment or the selection of a single reference genome. 3) It is a reference free method, which facilitates analyses of more genomes that are more distantly related than an alignment-based or reference-genome based approach to find SNPs and can analyze together a set of finished genomes, genome assemblies, and genomes that are at the raw read stage. | Gardner SN, Hall BG. When whole-genome alignments just won't work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes. PLoS One. 2013 Dec 9;8(12):e81760. doi: 10.1371/journal.pone.0081760. eCollection 2013. PubMed PMID: 24349125; PubMed Central PMCID: PMC3857212
| 2013 | 99 |
|
| 82 |
MirSNPhttp://cmbi.bjmu.edu.cn/mirsnp |
Provides a collection of human SNPs predicted in predicted miRNA-mRNA binding sites and can identify the putative miRNA-related SNPs from GWAS and eQTLs researches. | Liu C, Zhang F, Li T, Lu M, Wang L, Yue W, Zhang D. MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs. BMC Genomics. 2012 Nov 23;13:661. doi: 10.1186/1471-2164-13-661. PubMed PMID: 23173617; PubMed Central PMCID: PMC3582533
| 2012 | 99 |
URL not working (as on 12 Dec 2023) |
| 83 |
ASSIsThttp://compbiotoolbox.fmach.it/assist/ |
Automated SNP scoring tool, used for filtering of Illumina Infinium/BeadExpress based SNP markers. | was used in one paper didn't find the publishing paper yet.
| Not available | 99 |
Downloadable. URL not working (as on 19 Feb 2017); confirmed in Dec 2023 |
| 84 |
LD Hubhttp://ldsc.broadinstitute.org/ |
Centralised database that performs LD score regression analysis which maximizes the potential of summary level GWAS data for SNP heritability. | Zheng J, Erzurumluoglu AM, Elsworth BL, Kemp JP, Howe L, Haycock PC, Hemani G, Tansey K, Laurin C, Pourcain BS, Warrington NM. LD Hub: a centralized database and web interface to perform LD score regression that maximizes the potential of summary level GWAS data for SNP heritability and genetic correlation analysis. Bioinformatics. 2016 Sep 22:btw613. PubMed PMID: 27663502
| 2016 | 99 |
Need to log-in through a google account. URL not working (as on 19 Feb 2017); confirmed in Dec 2023 |
| 85 |
ALOHOMORAhttp://gmc.mdc-berlin.de/alohomora/ |
Performs genome-wide linkage studies with high-density single nucleotide polymorphism (SNP) marker panels like the Affymetrix GeneChip Human Mapping 10K Array. | Ruschendorf F, Nurnberg P. ALOHOMORA: a tool for linkage analysis using 10K SNP array data. Bioinformatics. 2005 May 1;21(9):2123-5. Epub 2005 Jan 12. PubMed PMID: 15647291.
| 2005 | 100 |
Freely downloadable |
| 86 |
2LDhttp://www.hgmp.mrc.ac.uk/~jzhao |
| Zhao JH. 2LD, GENECOUNTING and HAP: Computer programs for linkage disequilibrium analysis. Bioinformatics. 2004 May 22;20(8):1325-6. Epub 2004 Feb 10. PubMed PMID: 14871868.
| 2004 | 100 |
URL not working as on 30 Nov 2013 (confirmed in 2017 and 2023) |
| 87 |
2SNPhttp://alla.cs.gsu.edu/~software/2SNP/ |
1) Explores disease susceptibility prediction on genotype/haplotype data. 2) Provides phasing method based on 2-SNP haplotypes and also assists in tag selection. | Brinza D, Zelikovsky A. 2SNP: scalable phasing method for trios and unrelated individuals. IEEE/ACM Trans Comput Biol Bioinform. 2008 Apr-Jun;5(2):313-8. PubMed PMID: 18451440.
| 2008 | 100 |
Freely downloadable. URL not working as on 31 Aug 2016 (confirmed in 2017 and 2023) |
| 88 |
ACCUSAftp://bbc.mdc-berlin.de/software |
It considers both the read qualities as well as the reference genome's quality for detecting SNPs in the sequenced genome. | Frohler S, Dieterich C. ACCUSA--accurate SNP calling on draft genomes. Bioinformatics. 2010 May 15;26(10):1364-5. Epub 2010 Apr 1. PubMed PMID: 20363730.
| 2010 | 100 |
Freely downloadable. URL not working in 2019 and 2023 |
| 89 |
AssociationViewerhttp://sourceforge.net/projects/associationview/ |
A Java application to display SNPs in a genomic context. | Martin O, Valsesia A, Telenti A, Xenarios I, Stevenson BJ. AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context. Bioinformatics. 2009 Mar 1;25(5):662-3. Epub 2009 Jan 25. PubMed PMID: 19168913
| 2009 | 100 |
Freely downloadable |
| 90 |
AtPIDhttp://atpid.biosino.org/ |
Annotates Arabidopsis thaliana proteome along with information on the SNP phenotype. | Cui J, Li P, Li G, Xu F, Zhao C, Li Y, Yang Z, Wang G, Yu Q, Li Y, Shi T. AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology. Nucleic Acids Res. 2008 Jan;36(Database issue):D999-1008. Epub 2007 Oct 25. PubMed PMID: 17962307.
| 2008 | 100 |
URL not working (as on 30 Nov 2013), (confirmed in 2017 and 2023) |
| 91 |
AutoSNPahttp://dna.leeds.ac.uk/autosnpa/ |
Visual analysis of SNP data and identification of autozygous chromosomal regions. | Carr IM, Flintoff KJ, Taylor GR, Markham AF, Bonthron DT. Interactive visual analysis of SNP data for rapid autozygosity mapping in consanguineous families. Hum Mutat. 2006 Oct;27(10):1041-6. PubMed PMID: 16941472.
| 2006 | 100 |
Freely downloadable. URL not working in 2019 and 2023 |
| 92 |
BEAPhttp://www.animalgenome.org/tools/beap/index.html |
Provides SNP discovery and analysis of linkage disequilibrium. | Koltes JE, Hu ZL, Fritz E, Reecy JM. BEAP: The BLAST Extension and Alignment Program- a tool for contig construction and analysis of preliminary genome sequence. BMC Res Notes. 2009 Jan 22;2:11. PubMed PMID: 19159488.
| 2009 | 100 |
Freely downloadable |
| 93 |
Bovine SNP Retrieverhttp://www.itb.cnr.it/bovine_snp_retriever/ |
Retrieves bovine SNPs and related information | Panzitta F, Caprera A, Merelli I, Milanesi L, Williams JL, Lazzari B, Stella A. Mining the bovine genome with the "Bovine SNP Retriever". J Hered. 2008 Nov-Dec;99(6):696-8. Epub 2008 Jun 9. PubMed PMID: 18544553.
| 2008 | 100 |
Online |
| 94 |
CandiSNPerhttp://www2.hu-berlin.de/wikizbnutztier/software/CandiSNPer/ |
1) Facilitates the selection of candidate SNPs associated with a disease or another trait of interest. It characterizes SNPs that are located in the vicinity of a start SNP. 2) It computes max LD around start SNP. 3) Information about molecular consequences of SNPs & the genes located in the LD region. | Schmitt AO, Assmus J, Bortfeldt RH, Brockmann GA. CandiSNPer: a web tool for the identification of candidate SNPs for causal variants. Bioinformatics. 2010 Apr 1;26(7):969-70. Epub 2010 Feb 19. PubMed PMID: 20172942.
| 2010 | 100 |
Input- rs ID species-human but regional population specific only. Free, online & user friendly. Divides all SNPs & start SNP into various functional classes like coding, non coding, UTR's, 3' & 5' regions, etc. |
| 95 |
Catmaphttp://cran.r-project.org/web/packages/catmap/index.html |
| Nicodemus KK. Catmap: case-control and TDT meta-analysis package. BMC Bioinformatics. 2008 Feb 28;9:130. PubMed PMID: 18307795.
| 2008 | 100 |
Freely downloadable |
| 96 |
CLOUREhttp://imtech.res.in/~anand/cloure.html |
A visualization and exploration environment for non-synonymous coding single nucleotide polymorphisms (nsSNPs) data. | Kohli DK, Bachhawat AK. CLOURE: Clustal Output Reformatter, a program for reformatting ClustalX/ClustalW outputs for SNP analysis and molecular systematics. Nucleic Acids Res. 2003 Jul 1;31(13):3501-2. PubMed PMID: 12824353.
| 2003 | 100 |
URL not working as on 30 Nov 2013 (confirmed in 2017 and 2023) |
| 97 |
CLUMPhttp://www.smd.qmul.ac.uk/statgen/dcurtis/software.html |
Program designed to assess genetic case-control association studies. It performs: (1) analysis on multiple data files. (2) haplotype phasing. (3) analysis on insertion/deletion polymorphism data. (4) visualizing sliding window results integration with available genome annotations in the UCSC browser. | | Not available | 100 |
Freely downloadable. URL not working (as on Dec 2023) |
| 98 |
CLUMPHAPhttp://www.smd.qmul.ac.uk/statgen/dcurtis/software.html |
1) Performs association analysis of haplotypes to study casual variants. 2) Gives information about SNPs present within genes, which code for drug targets. 3) Provides combined information on drug target proteins (including enzyme, receptor, and agonists/antagonists), genes and SNPs. | Knight J, Curtis D, Sham PC. CLUMPHAP: a simple tool for performing haplotype-based association analysis. Genet Epidemiol. 2008 Sep;32(6):539-45. PubMed PMID: 18395815.
| 2008 | 100 |
Freely downloadable. URL not working (as on Dec 2023) |
| 99 |
easyLINKAGE-Plushttp://www.uni-wuerzburg.de/nephrologie/molecular_genetics/molecular_genetics.htm |
| Hoffmann K, Lindner TH. easyLINKAGE-Plus--automated linkage analyses using large-scale SNP data. Bioinformatics. 2005 Sep 1;21(17):3565-7. Epub 2005 Jul 12. PubMed PMID: 16014370.
| 2005 | 100 |
URL not working as on 30 Nov 2013 (confirmed in 2017 and 2023) |
| 100 |
Ecgenehttp://genome.ewha.ac.kr/ECgene/ |
Predicts the transcript structure, expression and functions in context to alternative splicing and annotates the association of SNP and alternative splicing. | Lee Y, Lee Y, Kim B, Shin Y, Nam S, Kim P, Kim N, Chung WH, Kim J, Lee S. ECgene: an alternative splicing database update. Nucleic Acids Res. 2007 Jan;35(Database issue):D99-103. Epub 2006 Nov 28. PubMed PMID: 17132829.
| 2007 | 100 |
Online. URL not working as on 30 Nov 2013 (confirmed in 2017 and 2023) |
| 101 |
EICO - Expression-based Imprint Candidate Organizerhttp://fantom2.gsc.riken.jp/EICODB/ |
| Nikaido I, Saito C, Wakamoto A, Tomaru Y, Arakawa T, Hayashizaki Y, Okazaki Y. EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D548-51. PubMed PMID: 14681478.
| 2004 | 100 |
URL not working as on 30 Nov 2013 (confirmed in 2017 and 2023) |
| 102 |
FastEpistasishttp://www.vital-it.ch/software/FastEpistasis/ |
It computes tests of epistasis for a large number of SNP pairs. | Schupbach T, Xenarios I, Bergmann S, Kapur K. FastEpistasis: a high performance computing solution for quantitative trait epistasis. Bioinformatics. 2010 Jun 1;26(11):1468-9. Epub 2010 Apr 7. PubMed PMID: 20375113.
| 2010 | 100 |
Freely downloadable |
| 103 |
FastMaphttp://cebc.unc.edu/fastmap.html |
Performs either single marker mapping (SMM) or haplotype association mapping (HAM) to locate genomic loci associated with a phenotypic variation. | Gatti DM, Shabalin AA, Lam TC, Wright FA, Rusyn I, Nobel AB. FastMap: fast eQTL mapping in homozygous populations. Bioinformatics. 2009 Feb 15;25(4):482-9. Epub 2008 Dec 17. PubMed PMID: 19091771.
| 2009 | 100 |
Freely downloadable. URL not working as on 30 Nov 2013 (confirmed in 2017 and 2023) |
| 104 |
Flapjackhttp://bioinf.scri.ac.uk/flapjack/ |
1) For graphical genotyping and haplotype visualization. 2) Based on the input of map, genotype and trait data, it is able to provide a number of alternative graphical genotype views with individual alleles coloured by state, frequency or similarity to a given standard line. 3) Flapjack supports a range of interactions with the data, including graphically moving lines or markers around the display, insertions or deletions of data, and sorting or clustering of lines by either genotype similarity to other lines, or by trait scores. 4) Any map based information such as QTL positions can be aligned against graphical genotypes to identify associated haplotypes. | Milne I, Shaw P, Stephen G, Bayer M, Cardle L, Thomas WT, Flavell AJ, Marshall D. Flapjack--graphical genotype visualization. Bioinformatics. 2010 Dec 15;26(24):3133-4. Epub 2010 Oct 18. PubMed PMID: 20956241.
| 2010 | 100 |
Freely downloadable |
| 105 |
Foragehttp://biobase.biotech.kth.se/forage/ |
| Unneberg P, Stromberg M, Sterky F. SNP discovery using advanced algorithms and neural networks. Bioinformatics. 2005 May 15;21(10):2528-30. Epub 2005 Mar 3. PubMed PMID: 15746291.
| 2005 | 100 |
URL not working as on 30 Nov 2013 (confirmed in 2017 and 2023) |
| 106 |
Frequency Finderhttp://bluegenes.bsd.uchicago.edu/frequencyfinder/ |
1) It provides a single, user-friendly interface for retrieving allele frequencies for large batches of SNPs from multiple data sources. 2) To retrieve mapping data and real-time data from the ABI database. 3) Resources for allele frequency data include 3 publicly available databases i.e TSC, dbSNP, ALFRED, HGVbase & Celera genomics. 4) Includes several methods to output the data, including on-screen and as a compressed text file. | Nguyen TH, Liu C, Gershon ES, McMahon FJ. Frequency Finder: a multi-source web application for collection of public allele frequencies of SNP markers. Bioinformatics. 2004 Feb 12;20(3):439-43. Epub 2004 Jan 22. PubMed PMID: 14960477.
| 2004 | 100 |
Online & new version (v2.1) Freely downloadable. URL not working (as on 30 Nov 2013); confirmed in 2017 and 2023 |
| 107 |
Gene Resource Locatorhttp://grl.gi.k.u-tokyo.ac.jp |
Assembles gene maps, which provide information on gene-expression patterns, cis-elements, alternatively spliced transcript groups, SNP loci, etc. | Honkura T, Ogasawara J, Yamada T, Morishita S. The Gene Resource Locator: gene locus maps for transcriptome analysis. Nucleic Acids Res. 2002 Jan 1;30(1):221-5. PubMed PMID: 11752299.
| 2002 | 100 |
URL not working as on 30 Nov 2013 (confirmed in 2017 and 2023) |
| 108 |
GENECOUNTING1. http://www.hgmp.mrc.ac.uk/~jzhao 2. http://www.iop.kcl.ac.uk/IoP/Departments/PsychMed/GEpiBSt/software.shtml |
| Zhao JH. 2LD, GENECOUNTING and HAP: Computer programs for linkage disequilibrium analysis. Bioinformatics. 2004 May 22;20(8):1325-6. Epub 2004 Feb 10. PubMed PMID: 14871868.
| 2004 | 100 |
1st URL is not working (as on 30 Nov 2013); confirmed in 2023 |
| 109 |
genetic map position of SNPshttp://integrin.ucd.ie/cgi-bin/rs2cm.cgi |
It is an application, which determines the genetic map position in centiMorgans of SNPs from the Human Genome subset of the dbSNP database. | | Not available | 100 |
Online. URL not working as on Dec 2023 |
| 110 |
Genewindowhttp://genewindow.nci.nih.gov/Welcome |
| Staats B, Qi L, Beerman M, Sicotte H, Burdett LA, Packer B, Chanock SJ, Yeager M. Genewindow: an interactive tool for visualization of genomic variation. Nat Genet. 2005 Feb;37(2):109-10. PubMed PMID: 15678133.
| 2005 | 100 |
Online |
| 111 |
GENOTRACEhttp://genotrace.niob.knaw.nl/ |
Used in genetic studies to analyze individuals for codon-changing single nucleotide polymorphisms or mutations. | Berezikov E, Plasterk RH, Cuppen E. GENOTRACE: cDNA-based local GENOme assembly from TRACE archives. Bioinformatics. 2002 Oct;18(10):1396-7. PubMed PMID: 12376385.
| 2002 | 100 |
Online. URL not working as on Feb 2017 and confirmed in Dec 2023. |
| 112 |
GenotypeColourhttp://www.med.unibs.it/~barlati/GenotypeColour/ |
Provides coloured visualization, which is useful in displaying and comparing SNP and CNV genomic data. | Barlati S, Chiesa S, Magri C. "GenotypeColour": colour visualisation of SNPs and CNVs. BMC Bioinformatics. 2009 Feb 4;10:49. PubMed PMID: 19193232.
| 2009 | 100 |
Freely downloadable. URL opens a different site as on Dec 2023. |
| 113 |
GenoWatchhttp://genepipe.ngc.sinica.edu.tw/genowatch |
A bioinformatics pipeline for large-scale human genomic variation studies. | Chen YH, Liu CK, Chang SC, Lin YJ, Tsai MF, Chen YT, Yao A. GenoWatch: a disease gene mining browser for association study. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W336-40. Epub 2008 Apr 25. PubMed PMID: 18440974
| 2008 | 100 |
Online. URL not working as on Dec 2023 |
| 114 |
GEN-SNiPwww.argusbio.com/sooryakiran/gensnip/gensnip.php |
Identifies variations in a set of test DNA sequences with respect to a standard reference sequence and generates a list of substitutions, insertions and deletions for each test sequences. | Whyte DB, Nair GG, Nair AS, Oommen OV. GEN-SNiP: an online tool to find polymorphisms in a genome. In Silico Biol. 2009;9(5-6):333-6. doi: 10.3233/ISB-2009-0401. PubMed PMID: 22430435
| Not available | 100 |
URL not working as on 30 Nov 2013 (confirmed in 2017 and 2023) |
| 115 |
GEVALT - GEnotype Visualization and ALgorithmic Toolhttp://acgt.cs.tau.ac.il/gevalt/ |
Performs genotype phasing, tag SNP selection, LD and haplotype block- analysis, association tests and visual display. | Davidovich O, Kimmel G, Shamir R. GEVALT: an integrated software tool for genotype analysis. BMC Bioinformatics. 2007 Feb 1;8:36. PubMed PMID: 17270038.
| 2007 | 100 |
Freely downloadable. Requires installation of JRE v1.5 or later version. |
| 116 |
GLIDERS- Genome-wide LInkage DisEquilibrium Repository and Search enginehttp://mather.well.ox.ac.uk/GLIDERS/ |
Retrieves genome-wide inter-SNP associations and explores LD patterns for any number of SNPs of interest and can be useful in identifying SNPs with long-range LD. | Lawrence R, Day-Williams AG, Mott R, Broxholme J, Cardon LR, Zeggini E. GLIDERS--a web-based search engine for genome-wide linkage disequilibrium between HapMap SNPs. BMC Bioinformatics. 2009 Oct 31;10:367. PubMed PMID: 19878600.
| 2009 | 100 |
Online. URL not working as on 30 Nov 2013 (confirmed in 2017 and 2023) |
| 117 |
GOLDsurferwww.umbio.com |
A java-based analysis and graphics program for three-dimensional plotting of linkage disequilibrium (LD) and facilitates the interpretation of LD patterns. It is embedded with the Evince graphical software package. | Pettersson F, Jonsson O, Cardon LR. GOLDsurfer: three dimensional display of linkage disequilibrium. Bioinformatics. 2004 Nov 22;20(17):3241-3. Epub 2004 Jun 16. PubMed PMID: 15201180.
| 2004 | 100 |
Online registration. Opens to different URL "http://www.prediktera.se/" |
| 118 |
GSA-SNPhttp://gsa.muldas.org/ |
1)The gene set analysis methods were introduced to GWA studies to address the association of gene sets that share common biological functions. 2) A general approach for GSA in GWA analysis and a stand-alone software GSA-SNP that implements three widely used GSA methods. | Nam D, Kim J, Kim SY, Kim S. GSA-SNP: a general approach for gene set analysis of polymorphisms. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W749-54. Epub 2010 May 25. PubMed PMID: 20501604.
| 2010 | 100 |
Freely downloadable. URL not working as on Dec 2023 |
| 119 |
GSEA-SNPhttp://www.nr.no/pages/samba/area_emr_smbi_gseasnp |
Analysis of the SNP data from association studies by the application of gene set enrichment analysis (GSEA) method. | Holden M, Deng S, Wojnowski L, Kulle B. GSEA-SNP: applying gene set enrichment analysis to SNP data from genome-wide association studies. Bioinformatics. 2008 Dec 1;24(23):2784-5. Epub 2008 Oct 14. PubMed PMID: 18854360.
| 2008 | 100 |
Freely downloadable. URL not working as on 30 Nov 2013 (confirmed in 2017 and 2023) |
| 120 |
GWAS GUIhttp://www.sph.umich.edu/csg/weich/browser/ |
| Chen W, Liang L, Abecasis GR. GWAS GUI: graphical browser for the results of whole-genome association studies with high-dimensional phenotypes. Bioinformatics. 2009 Jan 15;25(2):284-5. Epub 2008 Nov 20. PubMed PMID: 19028721.
| 2009 | 100 |
Freely downloadable. URL not working as on 30 Nov 2013 (confirmed in 2017 and 2023) |
| 121 |
GWAsimulatorhttp://biostat.mc.vanderbilt.edu/wiki/Main/GWAsimulator |
It can simulate the genotype data for SNP chips that are used in genome-wide association (GWA) studies and provides more detailed LD information for case-control data or population samples. | Li C, Li M. GWAsimulator: a rapid whole-genome simulation program. Bioinformatics. 2008 Jan 1;24(1):140-2. Epub 2007 Nov 15. PubMed PMID: 18006546.
| 2008 | 100 |
Freely downloadable. URL not working as on 30 Nov 2013 (confirmed in 2017 and 2023) |
| 122 |
HAP1. http://www.hgmp.mrc.ac.uk/~jzhao 2. http://www.iop.kcl.ac.uk/IoP/Departments/PsychMed/GEpiBSt/software.shtml |
| Zhao JH. 2LD, GENECOUNTING and HAP: Computer programs for linkage disequilibrium analysis. Bioinformatics. 2004 May 22;20(8):1325-6. Epub 2004 Feb 10. PubMed PMID: 14871868.
| 2004 | 100 |
1st URL is not working (as on 30 Nov 2013); confirmed in 2023. 2nd URL opens to a college site. (Kings college London) |
| 123 |
HapBlockhttp://www.cmb.usc.edu/msms/HapBlock/ |
1) Estimates the block partition with minimum number of tag SNPs for the given criteria of blocks and tag SNPs. 2) Both haplotype data and genotype data from unrelated individuals and/or from general pedigrees can be analyzed. 3) The programs provide flexibility to include specific SNPs (e.g. non-synonymous SNPs) as tag SNPs. 4) It incorporates different definitions of haplotype block and different criteria for tag SNP selections for different applications. 5) It provides an interface that can take the output from other methods for haplotype block partitioning and tag SNP selection as input. | Zhang K, Qin Z, Chen T, Liu JS, Waterman MS, Sun F. HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms. Bioinformatics. 2005 Jan 1;21(1):131-4. Epub 2004 Aug 27. PubMed PMID: 15333454.
| 2005 | 100 |
Freely downloadable. URL not working as on 30 Nov 2013 (confirmed in 2017 and 2023) |
| 124 |
hapConstructorhttp://bioinformatics.med.utah.edu/Genie/hapConstructor.html |
| Abo R, Knight S, Wong J, Cox A, Camp NJ. hapConstructor: automatic construction and testing of haplotypes in a Monte Carlo framework. Bioinformatics. 2008 Sep 15;24(18):2105-7. Epub 2008 Jul 23. PubMed PMID: 18653522.
| 2008 | 100 |
Freely downloadable. URL not working as on 30 Nov 2013 (confirmed in 2017 and 2023) |
| 125 |
HaploBuildhttp://snp.bumc.bu.edu/modules.php?name=HaploBuild |
Builds haplotype by allowing the association of subsets of single nucleotide polymorphisms (SNPs). | Laramie JM, Wilk JB, DeStefano AL, Myers RH. HaploBuild: an algorithm to construct non-contiguous associated haplotypes in family based genetic studies. Bioinformatics. 2007 Aug 15;23(16):2190-2. Epub 2007 Jun 22. PubMed PMID: 17586827.
| 2007 | 100 |
Freely downloadable. URL not working as on 30 Nov 2013 (confirmed in 2017 and 2023) |
| 126 |
HaploSNPerhttp://www.bioinformatics.nl/tools/haplosnper/ |
Detects SNPs and alleles in the user-specified input sequences from both diploid and polyploid species. | Tang J, Leunissen JA, Voorrips RE, van der Linden CG, Vosman B. HaploSNPer: a web-based allele and SNP detection tool. BMC Genet. 2008 Feb 28;9:23. PubMed PMID: 18307806.
| 2008 | 100 |
Online. URL not working. HaploSNPer has been discontinued. |
| 127 |
HAPLOThttp://krunch.med.yale.edu/haplo/ |
Compares variations in linkage disequilibrium patterns, in tagSNP sets, and in SNP heterozygosities among populations, which can be useful to infer the evolutionary patterns among different populations. | Gu S, Pakstis AJ, Kidd KK. HAPLOT: a graphical comparison of haplotype blocks, tagSNP sets and SNP variation for multiple populations. Bioinformatics. 2005 Oct 15;21(20):3938-9. Epub 2005 Aug 30. PubMed PMID: 16131520.
| 2005 | 100 |
Freely downloadable. URL not working as on Feb 2017; confirmed in Dec 2023 |
| 128 |
HapScopehttp://lpg.nci.nih.gov/lpg_small/protocols/HapScope/ |
| Zhang J, Rowe WL, Struewing JP, Buetow KH. HapScope: a software system for automated and visual analysis of functionally annotated haplotypes. Nucleic Acids Res. 2002 Dec 1;30(23):5213-21. PubMed PMID: 12466546.
| 2002 | 100 |
The website is temporarily unavailable due to maintenance work (as on 4 Dec 2013). URL not working as on Dec 2023 |
| 129 |
IGG3 http://bioinfo.hku.hk/iggweb |
Integrates large genotype datasets across genome-wide association studies and HapMap project for whole-genome imputation and individual-level meta-analysis. | Li MX, Jiang L, Kao PY, Sham PC, Song YQ. IGG3: a tool to rapidly integrate large genotype datasets for whole-genome imputation and individual-level meta-analysis. Bioinformatics. 2009 Jun 1;25(11):1449-50. Epub 2009 Apr 3. PubMed PMID: 19346322.
| 2009 | 100 |
Freely downloadable. URL not working as on Aug 2016; confirmed in Feb 2017 and Dec 2023 |
| 130 |
InSNPhttp://www.mucosa.de/insnp/ |
Detects and provides compact visualization of the substitution and indel SNPs in sequencing traces. | Manaster C, Zheng W, Teuber M, Wächter S, Döring F, Schreiber S, Hampe J. InSNP: a tool for automated detection and visualization of SNPs and InDels. Hum Mutat. 2005 Jul;26(1):11-9. PubMed PMID: 15931688.
| 2005 | 100 |
Online registration |
| 131 |
INTERSNPhttp://intersnp.meb.uni-bonn.de/ |
Provides a genome-wide interaction analysis of the case-control SNP data. | Herold C, Steffens M, Brockschmidt FF, Baur MP, Becker T. INTERSNP: genome-wide interaction analysis guided by a priori information. Bioinformatics. 2009 Dec 15;25(24):3275-81. Epub 2009 Oct 16. PubMed PMID: 19837719.
| 2009 | 100 |
Freely downloadable. URL not working as on Dec 2023. |
| 132 |
is-rSNPhttp://enzyme.msd.nicta.com.au/is-rSNP/index.html |
Detects SNP in the regulatory region i.e. whether it is affecting the transcription factor binding site or not. | Macintyre G, Bailey J, Haviv I, Kowalczyk A. is-rSNP: a novel technique for in silico regulatory SNP detection. Bioinformatics. 2010 Sep 15;26(18):i524-30. PubMed PMID: 20823317.
| 2010 | 100 |
Online registration. URL not working as on Feb 2017; confirmed in Dec 2023 |
| 133 |
KinSNPhttp://bioinfo.bgu.ac.il/bsu/software/KinSNP/ |
1) For homozygosity mapping in families having the same lineage using SNP arrays. 2) It combines microarray genotype calls with the most updated SNP annotations, and searches for stretches of SNPs which are homozygous to the same allele in all ascertained sick individuals. (The input is- SNPs with rs ids & chromosome position & snp chip data). | Amir el-AD, Bartal O, Morad E, Nagar T, Sheynin J, Parvari R, Chalifa-Caspi V. KinSNP software for homozygosity mapping of disease genes using SNP microarrays. Hum Genomics. 2010 Aug;4(6):394-401. PubMed PMID: 20846928.
| 2010 | 100 |
Freely downloadable. URL not working as on Feb 2017; confirmed in Dec 2023 |
| 134 |
LD2SNPinghttp://bio.kuas.edu.tw/LD2NPing |
Provides SNP ID- and gene-centric online retrievals for SNP information, tag SNPs, provides RFLP enzyme information for SNP genotype and performs LD analysis. | Chang HW, Chuang LY, Chang YJ, Cheng YH, Hung YC, Chen HC, Yang CH. LD2SNPing: linkage disequilibrium plotter and RFLP enzyme mining for tag SNPs. BMC Genet. 2009 Jun 6;10:26. PMID:19500380
| 2009 | 100 |
URL not working (as on 30 Nov 2013) confirmed in Feb 2017 and Dec 2023 |
| 135 |
LDA - Linkage disequilibrium analyzerhttp://www.chgb.org.cn/lda/lda.htm |
| Ding K, Zhou K, He F, Shen Y. LDA--a java-based linkage disequilibrium analyzer. Bioinformatics. 2003 Nov 1;19(16):2147-8. PMID:14594722
| 2003 | 100 |
URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 136 |
LDB2000 http://cedar.genetics.soton.ac.uk/public html/LDB2000.html |
Information on sequence based integrated maps, which provide locations for genes and polymorphic markers in sequence and on genetic linkage, radiation hybrid and cytogenetic scales. | Ke X, Tapper W, Collins A. LDB2000: sequence-based integrated maps of the human genome. Bioinformatics. 2001 Jul;17(7):581-6. PMID:11448876
| 2001 | 100 |
- |
| 137 |
LdComparehttp://www.affymetrix.com/support/developer/tools/devnettools.affx |
A program that characterizes whole-genome LD structure on large number of SNPs in terms of single- and multiple-marker correlations. | Hao K, Di X, Cawley S. LdCompare: rapid computation of single- and multiple-marker r2 and genetic coverage. Bioinformatics. 2007 Jan 15;23(2):252-4. Epub 2006 Dec 5. PMID:17148510
| 2007 | 100 |
Online registration. URL not working as on Dec 2023 |
| 138 |
Libsequencehttp://www.molpopgen.org/software/libsequence.html |
A C++ library, which is designed to aid in writing applications for genomics and evolutionary genetics and performs the analysis of SNP data and sequence divergence. | Thornton K. Libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics. 2003 Nov 22;19(17):2325-7. PMID:14630667
| 2003 | 100 |
Freely downloadable. URL not working in August 2016; confirmed in Feb 2017 and Dec 2023 |
| 139 |
LS-SNPhttp://modbase.compbio.ucsf.edu/LS-SNP/ |
It annotates nsSNPs and is useful in identifying candidate functional SNPs within a gene, haplotype or pathway and in probing molecular mechanisms responsible for functional impacts of nsSNPs. | Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, Haussler D, Sali A. LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics. 2005 Jun 15;21(12):2814-20. Epub 2005 Apr 12. PubMed PMID: 15827081
| 2005 | 100 |
Online |
| 140 |
LS-SNP/PDBhttp://ls-snp.icm.jhu.edu/ls-snp-pdb/ |
Provides information useful for identifying amino-acid changing SNPs (nsSNPs) that have an impact on biological function. | Ryan M, Diekhans M, Lien S, Liu Y, Karchin R. LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. Bioinformatics. 2009 Jun 1;25(11):1431-2. Epub 2009 Apr 15. PMID:19369493
| 2009 | 100 |
Online. URL not working as on Dec 2023 |
| 141 |
MAGIChttp://cogent.iop.kcl.ac.uk/ MaGIC.cogx |
| Simpson CL, Hansen VK, Sham PC, Collins A, Powell JF, Al-Chalabi A. MaGIC: a program to generate targeted marker sets for genome-wide association studies. Biotechniques. 2004 Dec;37(6):996-9. PMID:15597550
| 2004 | 100 |
Freely downloadable. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 142 |
MapNexthttp://evolution.sysu.edu.cn/english/software/mapnext.htm |
A comprehensive tool for both spliced and unspliced alignments of short reads and automated SNP detection from population sequences. | Bao H, Xiong Y, Guo H, Zhou R, Lu X, Yang Z, Zhong Y, Shi S. MapNext: a software tool for spliced and unspliced alignments and SNP detection of short sequence reads. BMC Genomics. 2009 Dec 3;10 Suppl 3:S13. PMID:19958476
| 2009 | 100 |
URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 143 |
MAVIANThttp://snp.agrsci.dk/maviant |
It is a platform-independent Multipurpose Alignment VIewing and Annotation Tool, which provides a web-based DNA chromatogram and contig browser that can assist in the evaluation and selection of candidate SNPs. | Panitz F, Stengaard H, Hornshøj H, Gorodkin J, Hedegaard J, Cirera S, Thomsen B, Madsen LB, Høj A, Vingborg RK, Zahn B, Wang X, Wang X, Wernersson R, Jorgensen CB, Scheibye-Knudsen K, Arvin T, Lumholdt S, Sawera M, Green T, Nielsen BJ, Havgaard JH, Brunak S, Fredholm M, Bendixen C. SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation. Bioinformatics. 2007 Jul 1;23(13):i387-91. PubMed PMID: 17646321.
| 2007 | 100 |
URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 144 |
MedRefSNPhttp://www.medclue.com/ medrefsnp |
Provides enhanced and integrated information of the published SNPs by using its genomic and functional aspects. | Rhee H, Lee JS. MedRefSNP: a database of medically investigated SNPs. Hum Mutat. 2009 Mar;30(3):E460-6. PMID:19105187
| 2009 | 100 |
URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 145 |
MicroSNiPerhttp://cbdb.nimh.nih.gov/microsniper/ |
It examines the 3'-untranslated region and predicts if a SNP within the target site will disrupt or enhance a microRNA binding site. | Barenboim M, Zoltick BJ, Guo Y, Weinberger DR. MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets. Hum Mutat. 2010 Nov;31(11):1223-32. doi: 10.1002/humu.21349. Epub 2010 Oct 7. PMID: 20809528
| 2010 | 100 |
Online. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 146 |
Minimotif miner 2nd releasehttp://mnm.engr.uconn.edu |
Assists in the prediction of motif-based functions in user-supplied protein queries and also provides expanded SNP analysis. | Rajasekaran S, Balla S, Gradie P, Gryk MR, Kadaveru K, Kundeti V, Maciejewski MW, Mi T, Rubino N, Vyas J, Schiller MR. Minimotif miner 2nd release: a database and web system for motif search. Nucleic Acids Res. 2009 Jan;37(Database issue):D185-90. Epub 2008 Oct 31. PubMed PMID: 18978024.
| 2009 | 100 |
Online. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 147 |
MOCSphaserhttp://emu.src.riken.jp/ |
1) Finds frequencies of haplotypes composed of allelic copy numbers and SNP alleles at multiple CNV and SNP loci from the Mixture-data-Of-Cnv-Snp. 2) Also, calculates individual diplotypes and its respective frequencies. 3) Finds diplotype frequencies calculated from the haplotype frequencies under Hardy-Weinberg equilibrium. | Kato M, Nakamura Y, Tsunoda T. MOCSphaser: a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data. Bioinformatics. 2008 Jul 15;24(14):1645-6. Epub 2008 May 20. PubMed PMID: 18492685.
| 2008 | 100 |
Freely downloadable |
| 148 |
Mouse SNP Minerhttp://bioinfo.embl.it/SnpApplet/ |
Detailed information on the mouse functional SNPs and comprises of a runtime graphical display that allows chromosome walking, in-and-out zooming, and jumping between adjacent SNPs. | Reuveni E, Ramensky VE, Gross C. Mouse SNP Miner: an annotated database of mouse functional single nucleotide polymorphisms. BMC Genomics. 2007 Jan 21;8:24. PubMed PMID: 17239255.
| 2007 | 100 |
Online (needs JAVA platform). URL not working as on Dec 2023 |
| 149 |
MQScore_SNPhttp://mga.bionet.nsc.ru/soft/MQscore_SNP/ |
Performs multipoint parametric linkage analysis of quantitative traits using SNPs in large pedigrees without loops (linkage of triats, which are affected by multiple genes is studied by SNP markers/genotypes of large pedigree). | Axenovich TI, Aulchenko YS. MQScore_SNP software for multipoint parametric linkage analysis of quantitative traits in large pedigrees. Ann Hum Genet. 2010 May;74(3):286-9. PubMed PMID: 20529018.
| 2010 | 100 |
Freely downloadable. URL not working as on Dec 2023 |
| 150 |
MutaGeneSyshttp://www1.cs.columbia.edu/~jds1/MutaGeneSys/ |
It uses genome-wide genotype data to estimate individual disease susceptibility; it accepts SNP data of individuals as query input and delivers disease susceptibility hypotheses. | Stoyanovich J, Pe'er I. MutaGeneSys: estimating individual disease susceptibility based on genome-wide SNP array data. Bioinformatics. 2008 Feb 1;24(3):440-2. Epub 2007 Nov 29. PubMed PMID: 18048395.
| 2008 | 100 |
Freely downloadable |
| 151 |
Mutation Checkerhttp://mutation.sanbi.ac.za/checker |
| | Not available | 100 |
URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 152 |
Mutation@A Glancehttp://rapid.rcai.riken.jp/mutation/ |
A tool for mutation analysis of causative genes of human diseases. | Hijikata A, Raju R, Keerthikumar S, Ramabadran S, Balakrishnan L, Ramadoss SK, Pandey A, Mohan S, Ohara O. Mutation@A Glance: an integrative web application for analysing mutations from human genetic diseases. DNA Res. 2010 Jun;17(3):197-208. Epub 2010 Apr 1. PubMed PMID: 20360267.
| 2010 | 100 |
Online. URL not working (as on Aug 2016); confirmed in Feb 2017 and Dec 2023
URL not working (as on 24 April 2014) |
| 153 |
novoSNPhttp://www.molgen.ua.ac.be/bioinfo/novosnp/ |
Detects variations (SNPs and short INDELs) in resequencing projects. It takes a reference sequence and a number of sequencing trace files as input, and generates a list of possible variations with a quality score and also allows the user to easily filter, sort and check the variations (visually). | Weckx S, Del-Favero J, Rademakers R, Claes L, Cruts M, De Jonghe P, Van Broeckhoven C, De Rijk P. novoSNP, a novel computational tool for sequence variation discovery. Genome Res. 2005 Mar;15(3):436-42. PubMed PMID: 15741513.
| 2005 | 100 |
Freely downloadable. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 154 |
Oryza SNPhttp://www.oryzasnp.org/ |
Provides detailed information on the genetic variation present within and between diverse rice cultivars and landraces. | McNally KL, Bruskiewich R, Mackill D, Buell CR, Leach JE, Leung H. Sequencing multiple and diverse rice varieties. Connecting whole-genome variation with phenotypes. Plant Physiol. 2006 May;141(1):26-31. PubMed PMID: 16684934.
| 2006 | 100 |
Online |
| 155 |
Panseqhttp://76.70.11.198/panseq |
Finds SNPs within the core genome of the pan-genome and also determines the distribution of accessory genomic regions. | Laing C, Buchanan C, Taboada EN, Zhang Y, Kropinski A, Villegas A, Thomas JE, Gannon VP. Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions. BMC Bioinformatics. 2010 Sep 15;11:461. PubMed PMID: 20843356.
| 2010 | 100 |
Online. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 156 |
PANTHER Coding SNP Analysis Toolhttp://www.pantherdb.org/tools/csnpScoreForm.jsp |
Calculates the functional impact of a particular nonsynonymous (amino-acid changing) coding SNP on the protein. It estimates the subPSEC (substitution position-specific evolutionary conservation) score based on an alignment of evolutionarily related proteins. | | Not available | 100 |
Online |
| 157 |
ParaHaplohttp://en.sourceforge.jp/projects/parallelgwas/releases/ |
Conducts haplotype-based genome-wide association studies and analyzes the multiple comparisons at multiple SNP loci in linkage disequilibrium by treating linked loci as one haplotype block. | Misawa K, Kamatani N. ParaHaplo 2.0: a program package for haplotype-estimation and haplotype-based whole-genome association study using parallel computing. Source Code Biol Med. 2010 Jun 4;5:5. PubMed PMID: 20525312.
| 2010 | 100 |
Freely downloadable. URL changed to "https://osdn.net/projects/parallelgwas/releases/" (confirmed on 17 Feb 2017) |
| 158 |
PARSESNP- Project Aligned Related Sequences and Evaluate SNPshttp://www.proweb.org/parsesnp/ |
A tool for the display and analysis of polymorphisms in genes. It uses a reference DNA sequence, an exon/intron position model and a list of polymorphisms to determine the effects of these polymorphisms on the expressed gene product, as well as the changes in restriction enzyme recognition sites. | Taylor NE, Greene EA. PARSESNP: A tool for the analysis of nucleotide polymorphisms. Nucleic Acids Res. 2003 Jul 1;31(13):3808-11. PubMed PMID: 12824424.
| 2003 | 100 |
Online. URL not working as on Dec 2023 |
| 159 |
PEAS- Package for Elementary Analysis of SNP datahttp://www.picb.ac.cn/~xushua/index.files/Download_PEAS.htm |
A software package to facilitate the analyses of large data sets of single nucleotide polymorphisms (SNPs) for population genetics and molecular phylogenetics studies. | Xu S, Gupta S, Jin L. PEAS V1.0: a package for elementary analysis of SNP data. Mol Ecol Resour. 2010 Nov;10(6):1085-8. doi: 10.1111/j.1755-0998.2010.02862.x. PubMed PMID: 21565121.
| 2010 | 100 |
Downloadable |
| 160 |
pfSNPhttp://pfs.nus.edu.sg/%28S%28xnqct0xfimmbnwwr2yw53lec%29%29/PFS_LogIn_V2.aspx |
1) Finds putative function of the SNP and also projects whether the SNP has previously been associated with similar or other diseases/phenotypes/functions. 2) To select potentially functional SNPs in any gene-of-interest for studies associating a particular gene with phenotype. 3) Provides information on other previous reports that have examined the SNP-of-interest. 4) Provides information regarding the highest LD values (r2) of nearby pfSNPs. | Wang J, Ronaghi M, Chong SS, Lee CG. pfSNP: An integrated potentially functional SNP resource that facilitates hypotheses generation through knowledge syntheses. Hum Mutat. 2011 Jan;32(1):19-24. doi: 10.1002/humu.21331. PubMed PMID: 20672376.
| 2011 | 100 |
Registration required. URL not working as on Dec 2023 |
| 161 |
PicSNPhttp://picsnp.org |
| Chang H, Fujita T. PicSNP: a browsable catalog of nonsynonymous single nucleotide polymorphisms in the human genome. Biochem Biophys Res Commun. 2001 Sep 14;287(1):288-91. PubMed PMID: 11549289.
| 2001 | 100 |
Page not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 162 |
PolyDomshttp://polydoms.cchmc.org/polydoms/ |
Provides a method to derive a list of candidate SNPs, which can be evaluated in experimental or epidemiological studies for the impact on protein functions and disease risk associations. | Jegga AG, Gowrisankar S, Chen J, Aronow BJ. PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease. Nucleic Acids Res. 2007 Jan;35(Database issue):D700-6. Epub 2006 Nov 16. PubMed PMID: 17142238.
| 2007 | 100 |
URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 163 |
PolyScanhttp://genome.wustl.edu/pub/software/polyscan/ |
Predicts the affect of an amino acid substitution on protein function. [The input is a-protein sequence & amino acid, which is substituted by another & position of amino acid in the protein sequence]. | Chen K, McLellan MD, Ding L, Wendl MC, Kasai Y, Wilson RK, Mardis ER. PolyScan: an automatic indel and SNP detection approach to the analysis of human resequencing data. Genome Res. 2007 May;17(5):659-66. Epub 2007 Apr 6. PubMed PMID: 17416743.
| 2007 | 100 |
Online. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 164 |
PromoLignhttp://polly.wustl.edu/promolign/main.html |
Information on the correlation of SNPs with the TF sites, which assists in the functional evaluation of SNPs and provides graphical presentation for SNPs and transcription factor binding sites in the promoter region of genes in context to human-mouse orthologous sequence alignment. | Zhao T, Chang LW, McLeod HL, Stormo GD. PromoLign: a database for upstream region analysis and SNPs. Hum Mutat. 2004 Jun;23(6):534-9. PubMed PMID: 15146456.
| 2004 | 100 |
URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 165 |
PupasViewhttp://pupasview.ochoa.fib.es http://www.pupasnp.org. |
Provides information on the phenotypic effects caused by SNPs at both the translational and the transcriptional level. | Conde L, Vaquerizas JM, Ferrer-Costa C, de la Cruz X, Orozco M, Dopazo J. PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W501-5. PubMed PMID: 15980522
| 2005 | 100 |
URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 166 |
QuickSNPhttp://bioinformoodics.jhmi.edu/quickSNP.pl |
Provides an option to select only gene-centric SNPs from a chromosomal region in an automated fashion. Other useful features include SNP filtering based on inter-SNP distances and information regarding the availability of genotyping assays for SNPs and whether they are present on whole genome chips. | Grover D, Woodfield AS, Verma R, Zandi PP, Levinson DF, Potash JB. QuickSNP: an automated web server for selection of tagSNPs. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W115-20. Epub 2007 May 21. PubMed PMID: 17517769.
| 2007 | 100 |
URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 167 |
SEANhttp://http//zebrafish.doc.ic.ac.uk/Sean |
Predicts SNPs by using multiple sequence alignment, which are produced from EST clusters. | Huntley D, Baldo A, Johri S, Sergot M. SEAN: SNP prediction and display program utilizing EST sequence clusters. Bioinformatics. 2006 Feb 15;22(4):495-6. Epub 2005 Dec 15. PubMed PMID: 16357032.
| 2006 | 100 |
URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 168 |
Seq4SNPshttp://www.srl.cam.ac.uk/oncology/bio/s4shome.html |
Incorporates annotation for SNPs and repetitive elements and assists in the SNP-genotyping. | Seq4SNPs: new software for retrieval of multiple, accurately annotated DNA sequences, ready formatted for SNP assay design. Field HI, Scollen SA, Luccarini C, Baynes C, Morrison J, Dunning AM, Easton DF, Pharoah PD. BMC Bioinformatics. 2009 Jun 12;10:180.
| 2009 | 100 |
Message displayed that the new URL for the resource will be updated soon (as on 30 Nov 2013); not responding when checked in Dec 2023 |
| 169 |
SeqDoC- Sequence Difference of Chromatogramshttp://research.imb.uq.edu.au/seqdoc/ |
Allows comparison of ABI sequence chromatograms, which helps in the rapid identification of SNPs and point mutations and also highlights different characteristic of single base changes, including heterozygous SNPs and insertions and deletions. | Crowe ML. SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms. BMC Bioinformatics. 2005 May 31;6:133. PubMed PMID: 15927052.
| 2005 | 100 |
Online. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 170 |
SKM-SNPhttp://www.math.hkbu.edu.hk/~mng/SKM-SNP/SKM-SNP.html |
It is a SNP marker detection program, which identifies a set of relevant SNPs for the association between a disease and multiple marker genotypes. | Liu Y, Li M, Cheung YM, Sham PC, Ng MK. SKM-SNP: SNP markers detection method. J Biomed Inform. 2010 Apr;43(2):233-9. Epub 2009 Nov 17. PubMed PMID: 19925882.
| 2010 | 100 |
Downloadable. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 171 |
SLOPEhttp://www-genepi.med.utah.edu/suppl/SLOPE/index.html |
A fast and accurate tool for detecting structural variants like translocations and indels from targeted short-DNA reads. | Abel HJ, Duncavage EJ, Becker N, Armstrong JR, Magrini VJ, Pfeifer JD. SLOPE: a quick and accurate method for locating non-SNP structural variation from targeted next-generation sequence data. Bioinformatics. 2010 Nov 1;26(21):2684-8. Epub 2010 Sep 27. PubMed PMID: 20876606.
| 2010 | 100 |
Freely downloadable. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 172 |
SNEP - Simultaneous detection of both nucleotide and expression polymorphismshttp://www.ism.ac.jp/~fujisawa/SNEP/ |
It is a R-software, which facilitates the detection of both nucleotide and expression polymorphisms simultaneously. | Fujisawa H, Horiuchi Y, Harushima Y, Takada T, Eguchi S, Mochizuki T, Sakaguchi T, Shiroishi T, Kurata N. SNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip. BMC Bioinformatics. 2009 May 6;10:131. PubMed PMID: 19419536.
| 2009 | 100 |
Online. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 173 |
SNP Charthttp://www.snpchart.ca |
| Tebbutt SJ, Opushnyev IV, Tripp BW, Kassamali AM, Alexander WL, Andersen MI. SNP Chart: an integrated platform for visualization and interpretation of microarray genotyping data. Bioinformatics. 2005 Jan 1;21(1):124-7. Epub 2004 Aug 12. PubMed PMID: 15308543.
| 2005 | 100 |
URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 174 |
SNP cherry pickerAuthor ID: SD@oxagen.co.uk |
Assists in finding SNPs associated with an increased risk of disease. | Harris M, Martin JM, Peden JF, Rawlings CJ. SNP cherry picker: maximizing the chance of finding an association with a disease SNP. Bioinformatics. 2003 Nov 1;19(16):2141-3. PubMed PMID: 14594720.
| 2003 | 100 |
The reporting article claims that the software is available, free of charge, for academic use on request from the authors. |
| 175 |
SNP Cutterhttp://bioinfo.bsd.uchicago.edu/SNP_cutter.htm |
Designs primers for either natural PCR-RFLP or mismatch PCR-RFLP, to perform the assay on a batch of SNPs from the human genome. | Zhang R, Zhu Z, Zhu H, Nguyen T, Yao F, Xia K, Liang D, Liu C. SNP Cutter: a comprehensive tool for SNP PCR-RFLP assay design. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W489-92. PubMed PMID: 15980518.
| 2005 | 100 |
URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 176 |
SNP ID-infohttp://bio.kuas.edu.tw/snpid-info |
Provides an SNP ID by inputting the primers, genomic sequence, chromosome contig range and cytogenic band information for human, rat and mouse sequences with or without primers and serves to be a helpful platform for systematic SNP association studies. | Yang CH, Chuang LY, Cheng YH, Wen CH, Chang PL, Chang HW. SNP ID-info: SNP ID searching and visualization platform. OMICS. 2008 Sep;12(3):217-26. PubMed PMID: 18582176.
| 2008 | 100 |
Online. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 177 |
snp.plotterhttp://cbdb.nimh.nih.gov/~kristin/snp.plotter.html |
1) Produces images of genetic association results using single SNP and/or haplotype data with a corresponding LD heatmap in one correctly aligned graphic. 2) Plots single SNP and/or haplotype data and simultaneously plot multiple sets of results. 3) Figures are produced in two print sizes (3.5 and 7 inches) corresponding to one and two columns, respectively, on a printed page in resolution-independent formats (PDF and EPS) for ease of use in manuscript preparation. 4) Its figures can be easily imported into LaTeX documents, and due to the resolution-independent formats used, figures can be converted into raster image formats such as JPG, PNG and BMP without a loss in quality. 5) It includes options to display a linkage disequilibrium (LD) plot below the P-value plot using either the r2 or D0 LD metric, to set the X-axis to equal spacing or to use the physical map of markers, and to specify plot labels, colors, symbols and LD heatmap color scheme. | Luna A, Nicodemus KK. snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package. Bioinformatics. 2007 Mar 15;23(6):774-6. Epub 2007 Jan 18. PubMed PMID: 17234637.
| 2007 | 100 |
Freely downloadable. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 178 |
SNP@Domainhttp://snpnavigator.net/ |
Finds SNPs within protein domains with 2D and 3D maps and this visual annotation of SNPs is useful to interpret SNPs associated with diseases. | Han A, Kang HJ, Cho Y, Lee S, Kim YJ, Gong S. SNP@Domain: a web resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequences. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W642-4. PubMed PMID: 16845090.
| 2006 | 100 |
URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 179 |
SNP@Ethnoshttp://variome.kobic.re.kr/SNPatETHNIC/ |
Finds the ethnically variant single-nucleotide polymorphisms (ESNPs) from the genotype profile of the populations included in the International HapMap database. | Park J, Hwang S, Lee YS, Kim SC, Lee D. SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms. Nucleic Acids Res. 2007 Jan;35(Database issue):D711-5. Epub 2006 Nov 28. PubMed PMID: 17135185.
| 2007 | 100 |
Online. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 180 |
SNP@Evolutionhttp://bighapmap.big.ac.cn/ |
Integrates the heterozygosity (HET) of SNPs based on data of HapMap with the available data of integrated Haplotype Score (iHS) at levels of single SNPs, genes, and regions of chromosomes and focuses on the positive selection of the human genome. | Cheng F, Chen W, Richards E, Deng L, Zeng C. SNP@Evolution: a hierarchical database of positive selection on the human genome. BMC Evol Biol. 2009 Sep 5;9:221. PubMed PMID: 19732458
| 2009 | 100 |
Online & data can be downloaded for hapmap phase project. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 181 |
SNP@Promoterhttp://variome.kobic.re.kr/SNPatPromoter |
Identifies functional SNPs in the putative promoter regions. The database can be searched by three entries like- a) SNP identifier (rs number from dbSNP), b) by gene (gene name, gene symbol, refSeq ID), and c) by disease term. | Kim BC, Kim WY, Park D, Chung WH, Shin KS, Bhak J. SNP@Promoter: a database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions. BMC Bioinformatics. 2008;9 Suppl 1:S2. PubMed PMID: 18315851.
| 2008 | 100 |
URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 182 |
SNP_toolshttp://www.bioinformatics.org/snp-tools-excel/ |
Provides a basic genetic and epidemiological analysis of the SNP data and serves as a general add-in for the Microsoft Excel. | Chen B, Wilkening S, Drechsel M, Hemminki K. SNP_tools: A compact tool package for analysis and conversion of genotype data for MS-Excel. BMC Res Notes. 2009 Oct 23;2:214. PubMed PMID: 19852806.
| 2009 | 100 |
Downloadable |
| 183 |
SNP2CAPShttp://pgrc.ipk-gatersleben.de/snp2caps/ |
Provides detection of SNPs and Indels and facilitates the computational conversion of SNPs to CAPS (cleaved amplified polymorphic sequences) markers. | Thiel T, Kota R, Grosse I, Stein N, Graner A. SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development. Nucleic Acids Res. 2004 Jan 2;32(1):e5. PubMed PMID: 14704362.
| 2004 | 100 |
Downloadable |
| 184 |
SNP2RFLPhttp://genetics.bwh.harvard.edu/snp2rflp/ |
Extracts region-specific SNPs from the NCBI mouse SNP database, which are informative between the mouse strains and further identifies those SNPs that create restriction fragment length polymorphisms (RFLPs). | Beckstead WA, Bjork BC, Stottmann RW, Sunyaev S, Beier DR. SNP2RFLP: a computational tool to facilitate genetic mapping using benchtop analysis of SNPs. Mamm Genome. 2008 Oct-Dec;19(10-12):687-90. Epub 2008 Oct 29. PubMed PMID: 18958524.
| 2008 | 100 |
Freely downloadable. Message dispalyed "SNP2RFLP database is temporarily out of service (as on Dec 2023) |
| 185 |
SNP500Cancerhttp://variantgps.nci.nih.gov/cgfseq/pages/snp500.do |
Finds known or novel SNPs within genes, which are involved in cancer. | Packer BR, Yeager M, Burdett L, Welch R, Beerman M, Qi L, Sicotte H, Staats B, Acharya M, Crenshaw A, Eckert A, Puri V, Gerhard DS, Chanock SJ. SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D617-21. PubMed PMID: 16381944.
| 2006 | 100 |
Online. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 186 |
SNPAnalyzerhttp://snp.istech.info/istech/board/login_form.jsp |
| Yoo J, Seo B, Kim Y. SNPAnalyzer: a web-based integrated workbench for single-nucleotide polymorphism analysis. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W483-8. PubMed PMID: 15980517
| 2005 | 100 |
Online registration. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 187 |
SNPannotatorhttp://dna.leeds.ac.uk/snpannotator/ |
Provides physical as well as genetic map positions to SNPs, which are present in the Affymetrix genotype data. | | Not available | 100 |
Freely downloadable. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 188 |
SNPatorhttp://www.snpator.org/public/new_login/index.php |
Performs the analysis of SNPs along with associated genomic information (e. g. chromosome position). | Morcillo-Suarez C, Alegre J, Sangros R, Gazave E, de Cid R, Milne R, Amigo J, Ferrer-Admetlla A, Moreno-Estrada A, Gardner M, Casals F, Perez-Lezaun A, Comas D, Bosch E, Calafell F, Bertranpetit J, Navarro A. SNP analysis to results (SNPator): a web-based environment oriented to statistical genomics analyses upon SNP data. Bioinformatics. 2008 Jul 15;24(14):1643-4. Epub 2008 May 30. PubMed PMID: 18515823.
| 2008 | 100 |
Online registration. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 189 |
SNPboxhttp://www.snpbox.org/cgi-box/SNPbox.cgi |
1) Primers are designed for a well-defined target sequence, which can contain either known SNPs from public databases for validation (SNP module), coding regions indicated by aligning cDNA/EST sequences to the genomic DNA (exon module), or promoter or whole genomic regions (saturation module). 2) It has an interface to a local database where primer information of the genome-wide application can be retrieved. 3) The genomic sequence is aligned to a local copy of HGVbase using the BLAST algorithm to determine the positions of public SNPs. 4) For the exon module, cDNA/EST sequences are required that will be aligned to the genomic sequence using Spidey. 5) The data can be visualized in Ensembl's ContigView through a DAS annotation server and it requires SVG viewer to display all elements of the output page. | Weckx S, De Rijk P, Van Broeckhoven C, Del-Favero J. SNPbox: web-based high-throughput primer design from gene to genome. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W170-2. PubMed PMID: 15215373.
| 2004 | 100 |
Online. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 190 |
SNPdetectorhttp://lpg.nci.nih.go |
Tool for automated identification of SNPs and mutations, which is helpful in the genome-scale research. | Zhang J, Wheeler DA, Yakub I, Wei S, Sood R, Rowe W, Liu PP, Gibbs RA, Buetow KH. SNPdetector: a software tool for sensitive and accurate SNP detection. PLoS Comput Biol. 2005 Oct;1(5):e53. Epub 2005 Oct 28. PubMed PMID: 16261194.
| 2005 | 100 |
Online. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 191 |
SNPeffect v2.0http://snpeffect.vib.be/ |
A database for phenotyping human single nucleotide polymorphisms (SNPs) and mainly focuses on the molecular characterization and annotation of disease and polymorphism variants in the human proteome. | Reumers J, Maurer-Stroh S, Schymkowitz J, Rousseau F. SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs. Bioinformatics. 2006 Sep 1;22(17):2183-5. Epub 2006 Jun 29. PubMed PMID: 16809394.
| 2006 | 100 |
URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 192 |
SNPexphttp://app3.titan.uio.no/biotools/tool.php?app=snpexp |
Calculates and visualizes correlation between HapMap genotypes and gene expression levels. | Holm K, Melum E, Franke A, Karlsen TH. SNPexp - A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels. BMC Bioinformatics. 2010 Dec 17;11:600. PubMed PMID: 21167019.
| 2010 | 100 |
Online. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 193 |
SNPforID browserhttp://spsmart.cesga.es/help.php?dataSets[]=snpforid52 |
Information on population based SNP genotype data and summarizing all that information into the most common population genetics indices such as allele frequencies, heterozygosity, etc. | Amigo J, Phillips C, Lareu M, Carracedo A. The SNPforID browser: an online tool for query and display of frequency data from the SNPforID project. Int J Legal Med. 2008 Sep;122(5):435-40. Epub 2008 May 20. PubMed PMID: 18491122.
| 2008 | 100 |
Online |
| 194 |
SNPHarvesterhttp://bioinformatics.ust.hk/SNPHarvester.html |
Detects SNP-SNP interactions in GWA studies and serves to be useful in practical disease prognosis. | Yang C, He Z, Wan X, Yang Q, Xue H, Yu W. SNPHarvester: a filtering-based approach for detecting epistatic interactions in genome-wide association studies. Bioinformatics. 2009 Feb 15;25(4):504-11. Epub 2008 Dec 19. PubMed PMID: 19098029.
| 2009 | 100 |
Online |
| 195 |
SNPHunterhttp://www.hsph.harvard.edu/ppg/software.htm |
Software provides retrieval of SNP information and automatic SNP selection based on their physical position, function class and flanking sequences at user-defined lengths. | Niu T. SNPHunter: a versatile web-based tool for acquiring and managing single nucleotide polymorphisms. Methods Mol Biol. 2007;396:359-69. PubMed PMID: 18025704.
| 2007 | 100 |
Freely downloadable. Page not opening (as on Dec 2023) |
| 196 |
SNPLINKhttp://webdocs.cs.ualberta.ca/~ghlin/src/WebTools/haplotyping.php |
Identifies the chromosomal regions shared by family members by using the high density SNP genotype data and handles "tree pedigrees", which is useful to locate the shared chromosomal region(s), where the disease responsible gene(s) might reside. | Webb EL, Sellick GS, Houlston RS. SNPLINK: multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal. Bioinformatics. 2005 Jul 1;21(13):3060-1. Epub 2005 Apr 19. PubMed PMID: 15840706.
| 2005 | 100 |
- |
| 197 |
SNPmaskerhttp://bioinfo.ebc.ee/snpmasker/ |
Used for masking SNPs and repeats within the genome before primer and probe designing. | Andreson R, Puurand T, Remm M. SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W651-5. PubMed PMID: 16845091.
| 2006 | 100 |
Freely downloadable |
| 198 |
SNPNBhttp://bioinfo.vipbg.vcu.edu/SNPNB/ |
Efficiently handles genome-wide or chromosome-wide SNP data analysis and provides visualization of the bias patterns for SNPs or each type of SNPs. | Zhang F, Zhao Z. SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs). Bioinformatics. 2005 May 15;21(10):2517-9. Epub 2005 Mar 15. PubMed PMID: 15769840.
| 2005 | 100 |
Online. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 199 |
SNPrankhttp://insilico.utulsa.edu/snprank/ |
1) It ranks the importance of single nucleotide polymorphisms (SNPs) in a genetic association interaction network (GAIN). 2) Each SNP is ranked according to its contribution to phenotype, including its main effect and second- and higher-order gene-gene interactions. | Davis NA, Pandey A, McKinney BA. Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS. Bioinformatics. 2011 Jan 15;27(2):284-5. Epub 2010 Nov 25. PubMed PMID: 21115438.
| 2011 | 100 |
- |
| 200 |
SNPseekhttp://snp.wustl.edu/cgi-bin/SNPseek/index.cgi |
Information on human SNPs, frequencies, and annotation data. | | Not available | 100 |
Online |
| 201 |
SNPselectorhttp://primer.duhs.duke.edu/ |
It searches the Ensembl genes or genomic regions (taken as input) for available SNPs and prioritizes these SNPs based on their tagging for linkage disequilibrium, allele frequencies and source, function, regulatory potential and repeat status. | SNPselector: a web tool for selecting SNPs for genetic association studies. Xu H, Gregory SG, Hauser ER, Stenger JE, Pericak-Vance MA, Vance JM, Züchner S, Hauser MA. Bioinformatics. 2005 Nov 15;21(22):4181-6. Epub 2005 Sep 22. PMID:16179360
| 2005 | 100 |
Online. Website mentions- 'Page is retired from public domain' (as on 11 Nov 2013); confirmed in Dec 2023 |
| 202 |
SNPServerhttp://hornbill.cspp.latrobe.edu.au/snpdiscovery.html |
Uses BLAST to discover SNPs within DNA sequence data. | Savage D, Batley J, Erwin T, Logan E, Love CG, Lim GA, Mongin E, Barker G, Spangenberg GC, Edwards D. SNPServer: a real-time SNP discovery tool. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W493-5. PubMed PMID: 15980519.
| 2005 | 100 |
URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 203 |
SNPsetterhttp://dna.leeds.ac.uk/snpsetter/ |
Provides details on standardization of SNP data. | Carr IM, Sheridan E, Hayward BE, Markham AF, Bonthron DT. IBDfinder and SNPsetter: tools for pedigree-independent identification of autozygous regions in individuals with recessive inherited disease. Hum Mutat. 2009 Jun;30(6):960-7. PubMed PMID: 19405095.
| 2009 | 100 |
Freely downloadable. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 204 |
SNPsFinderhttp://snpsfinder.lanl.gov/ |
Facilitates the discovery of SNPs among closely related microorganisms. | Song J, Xu Y, White S, Miller KW, Wolinsky M. SNPsFinder--a web-based application for genome-wide discovery of single nucleotide polymorphisms in microbial genomes. Bioinformatics. 2005 May 1;21(9):2083-4. Epub 2005 Feb 3. PubMed PMID: 15691853.
| 2005 | 100 |
Freely downloadable. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 205 |
SNPSplicerhttp://www.ikmb.uni-kiel.de/snpsplicer/ |
Investigates the effects of SNPs on splicing | ElSharawy A, Manaster C, Teuber M, Rosenstiel P, Kwiatkowski R, Huse K, Platzer M, Becker A, Nürnberg P, Schreiber S, Hampe J. SNPSplicer: systematic analysis of SNP-dependent splicing in genotyped cDNAs. Hum Mutat. 2006 Nov;27(11):1129-34. PubMed PMID: 16937379.
| 2006 | 100 |
Online. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 206 |
MicroSNiPerhttp://cbdb.nimh.nih.gov/microsniper |
Predicts the impact of SNP on microRNA binding site and provides graphical representation of the results. | Barenboim M, Zoltick BJ, Guo Y, Weinberger DR. MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets. Hum Mutat. 2010 Nov;31(11):1223-32. doi: 10.1002/humu.21349. Epub 2010 Oct 7. PubMed PMID: 20809528.
| 2010 | 100 |
Online. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 207 |
SNPtoGOhttps://webtools.imbs.uni-luebeck.de/snptogo/ |
Provides characterization of SNPs based on Gene Ontology (GO) terms. | Schwarz DF, Hädicke O, Erdmann J, Ziegler A, Bayer D, Möller S. SNPtoGO: characterizing SNPs by enriched GO terms. Bioinformatics. 2008 Jan 1;24(1):146-8. Epub 2007 Nov 17. PubMed PMID: 18024970.
| 2008 | 100 |
Freely downloadable. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 208 |
SNPToolshttp://www.birc.au.dk/snptools |
Provides analysis and visualization of microarray data, mainly SNP array data. | Sorensen FJ, Andersen CL, Wiuf C. SNPTools: a software tool for visualization and analysis of microarray data. Bioinformatics. 2007 Jun 15;23(12):1550-2. Epub 2007 Mar 24. PubMed PMID: 17384422.
| 2007 | 100 |
URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 209 |
SOP3http://biodev.hgen.pitt.edu/SOP3/ |
A tool for designing oligonucleotide primers, which are used for analysis of SNPs within the genome. | Alexander AM, Pecoraro C, Styche A, Rudert WA, Benos PV, Ringquist S, Trucco M. SOP3: a web-based tool for selection of oligonucleotide primers for single nucleotide polymorphism analysis by Pyrosequencing. Biotechniques. 2005 Jan;38(1):87-94. PubMed PMID: 15679090.
| 2005 | 100 |
URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 210 |
StSNP - Structure SNPhttp://ilyinlab.org/StSNP/ |
Compares the structural non- synonymous SNP distributions in many proteins or protein complexes. | Uzun A, Leslin CM, Abyzov A, Ilyin V. Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W384-92. Epub 2007 May 30. PubMed PMID: 17537826.
| 2007 | 100 |
Online. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 211 |
Sumstathttp://www.well.ox.ac.uk/gs2/ |
| Manuscript under preparation as displayed on website.
| Not available | 100 |
Freely downloadable. URL not working (as on 11 Nov 2013) |
| 212 |
S2G - Syndrome to genehttp://fohs.bgu.ac.il/s2g/index.html |
1) Efficient tool to diagnose candidate genes for human diseases. 2) For linkage studies, it helps in finding related genes by using a query set of genes with the ability of choosing an area of the genome (using genes, SNP's or chromosome and physical location). | Gefen A, Cohen R, Birk OS. Syndrome to gene (S2G): in-silico identification of candidate genes for human diseases. Hum Mutat. 2010 Mar;31(3):229-36. PubMed PMID: 20052752.
| 2010 | 100 |
Online. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 213 |
TAGsterhttp://www.niehs.nih.gov/research/resources/software/tagster/ |
It selects, evaluates and visualizes LD tag SNPs both for single and multiple populations. | Xu Z, Kaplan NL, Taylor JA. TAGster: efficient selection of LD tag SNPs in single or multiple populations. Bioinformatics. 2007 Dec 1;23(23):3254-5. Epub 2007 Sep 7. PubMed PMID: 17827206.
| 2007 | 100 |
Freely downloadable. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 214 |
The SNP Consortium websitehttp://snp.cshl.org |
| Thorisson GA, Stein LD. The SNP Consortium website: past, present and future. Nucleic Acids Res. 2003 Jan 1;31(1):124-7. PubMed PMID: 12519964.
| 2003 | 100 |
Online. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 215 |
The SNP ratio testhttp://sourceforge.net/projects/snpratiotest/ |
The SNP ratio test is used to assess significant associations in genome-wide association studies. | O'Dushlaine C, Kenny E, Heron EA, Segurado R, Gill M, Morris DW, Corvin A. The SNP ratio test: pathway analysis of genome-wide association datasets. Bioinformatics. 2009 Oct 15;25(20):2762-3. Epub 2009 Jul 20. PubMed PMID: 19620097.
| 2009 | 100 |
Freely downloadable |
| 216 |
UTRscanhttp://itbtools.ba.itb.cnr.it/utrscan |
Computes SNPs in the 5′ and 3′ untranslated regions. | | Not available | 100 |
URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 217 |
VarDetecthttp://www4a.biotec.or.th/GI/tools/vardetect |
It is a sequence variation exploration tool, which automatically detects nucleotide variation from fluorescence based chromatogram traces. | Ngamphiw C, Kulawonganunchai S, Assawamakin A, Jenwitheesuk E, Tongsima S. VarDetect: a nucleotide sequence variation exploratory tool. BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S9. PubMed PMID: 19091032.
| 2008 | 100 |
Freely downloadable. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 218 |
Variant Name Mapperhttp://www.hugenavigator.net/HuGENavigator/startPageMapper.do |
Maps gene variant common names to their corresponding rs numbers, which is compiled from web sources like SNPedia, SNP500 cancer, ALFRED, HuGE Navigator, OMIM, etc. | Yu W, Ned R, Wulf A, Liu T, Khoury MJ, Gwinn M. The need for genetic variant naming standards in published abstracts of human genetic association studies. BMC Res Notes. 2009 Apr 14;2:56. doi: 10.1186/1756-0500-2-56. PubMed PMID: 19366450; PubMed Central PMCID: PMC2672936
| 2009 | 100 |
Online. URL not working (as on 31 Aug 2016); confirmed in Feb 2017 and Dec 2023 |
| 219 |
varLDhttp://www.nus-cme.org.sg/software/varld.html |
A program, which quantifies variation in linkage disequilibrium patterns between populations (Chinese, Malays and Indians). | Ong RT, Teo YY. varLD: a program for quantifying variation in linkage disequilibrium patterns between populations. Bioinformatics. 2010 May 1;26(9):1269-70. Epub 2010 Mar 22. PubMed PMID: 20308177.
| 2010 | 100 |
Freely downloadable. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 220 |
viewGenehttp://chakravarti.som.jhmi.edu/viewGene/viewGene.html |
A useful tool to aid in the visualization and characterization of sequence and polymorphism data. | Kashuk C, SenGupta S, Eichler E, Chakravarti A. ViewGene: a graphical tool for polymorphism visualization and characterization. Genome Res. 2002 Feb;12(2):333-8. PubMed PMID: 11827953.
| 2002 | 100 |
URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 221 |
WASP - Web-based Allele-Specific Primer designing toolhttp://bioinfo.biotec.or.th/WASP |
Designs allele-specific (AS) primers for detecting SNPs and mutations. | Wangkumhang P, Chaichoompu K, Ngamphiw C, Ruangrit U, Chanprasert J, Assawamakin A, Tongsima S. WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations. BMC Genomics. 2007 Aug 14;8:275. PubMed PMID: 17697334.
| 2007 | 100 |
Online |
| 222 |
WatCuthttp://watcut.uwaterloo.ca/watcut/watcut/template.php |
An online tool for SNP-RFLP analysis, which detects single nucleotide polymorphisms by introducing restriction sites that will cleave only one variant sequence. | | Not available | 100 |
Online. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 223 |
WGAViewerhttp://people.chgv.lsrc.duke.edu/~dg48//WGAViewer/ |
| Ge D, Zhang K, Need AC, Martin O, Fellay J, Urban TJ, Telenti A, Goldstein DB. WGAViewer: software for genomic annotation of whole genome association studies. Genome Res. 2008 Apr;18(4):640-3. Epub 2008 Feb 6. PubMed PMID: 18256235.
| 2008 | 100 |
Freely downloadable. URL not working (as on 7 Nov 2013). |
| 224 |
WHAPhttp://pngu.mgh.harvard.edu/~purcell/whap/ |
Provides analysis of SNP haplotype associations with qualitative and quantitative traits in samples of individuals with or without parental genotype data. | Purcell S, Daly MJ, Sham PC. WHAP: haplotype-based association analysis. Bioinformatics. 2007 Jan 15;23(2):255-6. Epub 2006 Nov 21. PubMed PMID: 17118959.
| 2007 | 100 |
Freely downloadable. URL not working (as on 30 Nov 2013); confirmed in Feb 2017 and Dec 2023 |
| 225 |
A cSNP Map and Database for Human Chromosome 21http://csnp.unige.ch/ |
Provides details on the SNPs within the cDNA sequences of human chromosome 21 | Deutsch S, Iseli C, Bucher P, Antonarakis SE, Scott HS. A cSNP map and database for human chromosome 21. Genome Res. 2001 Feb;11(2):300-7. PubMed PMID: 11157793
| 2001 | 100 |
Online. Page not responding (as on 12 Dec 2023) |
| 226 |
ALFREDhttp://alfred.med.yale.edu/alfred/index.asp |
A compilation of allele frequencies for DNA sequence polymorphisms in anthropologically defined human populations. | Rajeevan H, Osier MV, Cheung KH, Deng H, Druskin L, Heinzen R, Kidd JR, Stein S, Pakstis AJ, Tosches NP, Yeh CC, Miller PL, Kidd KK. ALFRED: the ALelle FREquency Database. Update. Nucleic Acids Res. 2003 Jan 1;31(1):270-1. PubMed PMID: 12519999.
| 2003 | 100 |
Online |
| 227 |
AutoSNPdbhttp://autosnpdb.qfab.org.au/ |
Provides information on SNPs present in crop plants like barley, brassica, wheat and rice. | Duran C, Appleby N, Clark T, Wood D, Imelfort M, Batley J, Edwards D. AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants. Nucleic Acids Res. 2009 Jan;37(Database issue):D951-3. Epub 2008 Oct 14. PubMed PMID: 18854357; PubMed Central PMCID: PMC2686484.
| 2009 | 100 |
Online. URL not working (as on 31 Aug 2016); confirmed in Feb 2017 and Dec 2023 |
| 228 |
BcSNPdbhttp://snugenome.snu.ac.kr/BtcSNP/ |
Provides information on bovine coding SNPs | Moon S, Shin HD, Cheong HS, Cho HY, Namgoong S, Kim EM, Han CS, Sung S, Kim H. BcSNPdb: bovine coding region single nucleotide polymorphisms located proximal to quantitative trait loci. J Biochem Mol Biol. 2007 Jan 31;40(1):95-9. PubMed PMID: 17244488.
| 2007 | 100 |
Online. URL not working (as on 31 Aug 2016); confirmed in Feb 2017 and Dec 2023 |
| 229 |
Bovine in silico SNP (IBISS) databasehttp://www.livestockgenomics.csiro.au/cow/ |
An interactive database of bovine ESTs, which shows putative SNPs, model bovine mRNAs, and their relation to both the human genome and bovine reference mRNA and protein sequences. | Hawken RJ, Barris WC, McWilliam SM, Dalrymple BP. An interactive bovine in silico SNP database (IBISS). Mamm Genome. 2004 Oct;15(10):819-27. PubMed PMID: 15520884.
| 2004 | 100 |
Online. URL not working (as on 31 Aug 2016); confirmed in Feb 2017 and Dec 2023 |
| 230 |
CaSNPhttp://cistrome.dfci.harvard.edu/CaSNP/ |
A collection of copy number alteration (CNA) from SNP arrays of 34 different cancer types. | Cao Q, Zhou M, Wang X, Meyer CA, Zhang Y, Chen Z, Li C, Liu XS. CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data. Nucleic Acids Res. 2011 Jan;39(Database issue):D968-74. Epub 2010 Oct 23. PubMed PMID: 20972221.
| 2011 | 100 |
Online. URL not working (as on 31 Aug 2016); confirmed in Feb 2017 and Dec 2023 |
| 231 |
CGDSNPdbhttp://cgd.jax.org/cgdsnpdb/ |
Provides information on more than 66 million SNPs from 136 strains of laboratory mice and also integrates the SNP data with nearby gene annotations, including crosslinks, using Ensembl and MGI annotations. | Hutchins LN, Ding Y, Szatkiewicz JP, Von Smith R, Yang H, de Villena FP, Churchill GA, Graber JH. CGDSNPdb: a database resource for error-checked and imputed mouse SNPs. Database (Oxford). 2010 Jul 6;2010:baq008. Print 2010. PubMed PMID: 20624716.
| 2010 | 100 |
Online. URL not working (as on 31 Aug 2016); confirmed in Feb 2017 and Dec 2023 |
| 232 |
CNVVdbhttp://cnvvdb.genomics.sinica.edu.tw/ |
| Chen FC, Chen YZ, Chuang TJ. CNVVdb: a database of copy number variations across vertebrate genomes. Bioinformatics. 2009 Jun 1;25(11):1419-21. Epub 2009 Mar 25. PubMed PMID: 19321736.
| 2009 | 100 |
Online. URL not working (as on 31 Aug 2016); confirmed in Feb 2017 and Dec 2023 |
| 233 |
dbDNVhttp://goods.ibms.sinica.edu.tw/DNVs/ |
Provides information on SNPs coupled with duplicated-gene nucleotide variants (DNVs) within the human genome. | Ho MR, Tsai KW, Chen CH, Lin WC. dbDNV: a resource of duplicated gene nucleotide variants in human genome. Nucleic Acids Res. 2011 Jan;39(Database issue):D920-5. Epub 2010 Nov 21. PubMed PMID: 21097891.
| 2011 | 100 |
Online. URL not working (as on 31 Aug 2016); confirmed in Feb 2017 and Dec 2023 |
| 234 |
dbSMRhttp://miracle.igib.res.in/dbSMR |
Provides information on the SNPs in and around predicted miRNA target sites within the human genome. | Hariharan M, Scaria V, Brahmachari SK. dbSMR: a novel resource of genome-wide SNPs affecting microRNA mediated regulation. BMC Bioinformatics. 2009 Apr 16;10:108. PubMed PMID: 19371411.
| 2009 | 100 |
Online. URL not working (as on 31 Aug 2016); confirmed in Feb 2017 and Dec 2023 |
| 235 |
DPDB - Drosophila polymorphism databasehttp://dpdb.uab.es/dpdb/dpdb.asp |
Provides a collection of all the existing polymorphic sequences in the Drosophila genus. | Casillas S, Petit N, Barbadilla A. DPDB: a database for the storage, representation and analysis of polymorphism in the Drosophila genus. Bioinformatics. 2005 Sep 1;21 Suppl 2:ii26-30. PubMed PMID: 16204116
| 2005 | 100 |
- |
| 236 |
FLYSNPdbhttp://flysnp.imp.ac.at/flysnpdb.php |
Provides a genome-wide map of single nucleotide polymorphisms present in the Drosophila genome. | Chen D, Berger J, Fellner M, Suzuki T. FLYSNPdb: a high-density SNP database of Drosophila melanogaster. Nucleic Acids Res. 2009 Jan;37(Database issue):D567-70. Epub 2008 Sep 10. PubMed PMID: 18784187.
| 2009 | 100 |
Online. URL not working (as on 31 Aug 2016); confirmed in Feb 2017 and Dec 2023 |
| 237 |
FESD - Functional Element SNPs Databasehttp://sysbio.kribb.re.kr:8080/fesd/index.jsp |
Information on SNPs present in the specific functional elements (such as promoter regions, CpG islands, 5'-untranslated regions (5'-UTRs), translation start sites, splice sites, coding exons, introns, etc.) of the human genic regions. | Kang HJ, Choi KO, Kim BD, Kim S, Kim YJ. FESD: a Functional Element SNPs Database in human. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D518-22. Erratum in: Nucleic Acids Res. 2005;33(1):449. PubMed PMID: 15608252.
| 2005 | 100 |
Online. URL not working (as on 31 Aug 2016); confirmed in Feb 2017 and Dec 2023 |
| 238 |
FunctSNPhttp://functsnp.sourceforge.net/index.html |
FunctSNP provides a unified bioinformatics resource to link SNPs with functional knowledge (e.g., genes, pathways, ontologies). | Goodswen SJ, Gondro C, Watson-Haigh NS, Kadarmideen HN. FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases. BMC Bioinformatics. 2010 Jun 9;11:311. PubMed PMID: 20534127.
| 2010 | 100 |
- |
| 239 |
Go!Polyhttp://61.139.84.5/gopoly/ |
Provides access to gene-related variation data in human. | Zhang G, Zhang S, Chen W, Qiu W, Wu H, Wang J, Luo J, Gu X, Cotton RG. Go!Poly: A gene-oriented polymorphism database. Hum Mutat. 2001 Nov;18(5):382-7. PubMed PMID: 11668631.
| 2001 | 100 |
URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 240 |
GoShhttp://www.itb.cnr.it/gosh/snps.php |
Provides detailed information on SNPs found in the goat and sheep genome. | Caprera A, Lazzari B, Stella A, Merelli I, Caetano AR, Mariani P. GoSh: a web-based database for goat and sheep EST sequences. Bioinformatics. 2007 Apr 15;23(8):1043-5. Epub 2007 Mar 24. PubMed PMID: 17384426.
| 2007 | 100 |
Online. URL not working (as on 31 Aug 2016); confirmed in Feb 2017 and Dec 2023 |
| 241 |
GWAS Analyzerhttp://nwrce.org/gwas-analyzer |
Provides access to the data from a genome-wide association study of human susceptibility to bacterial infection. | Fong C, Ko DC, Wasnick M, Radey M, Miller SI, Brittnacher M. GWAS analyzer: integrating genotype, phenotype and public annotation data for genome-wide association study analysis. Bioinformatics. 2010 Feb 15;26(4):560-4. Epub 2010 Jan 6. PubMed PMID: 20053839.
| 2010 | 100 |
Online. URL not working (as on 31 Aug 2016); confirmed in Feb 2017 and Dec 2023 |
| 242 |
HGBASE - Human Genic Bi-Allelic Sequenceshttp://hgbase.cgr.ki.se |
A database of SNPs and other variations in and around the human genes. | Brookes AJ. HGBASE--a unified human SNP database. Trends Genet. 2001 Apr;17(4):229. PubMed PMID: 11357826.
| 2001 | 100 |
URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 243 |
HGVbase - Human Genome Variation Databasehttp://hgvbase.cgb.ki.se/ |
Important curated repository of nucleotide polymorphisms in humans with a goal to facilitate genotype-phenotype association analyses. | Fredman D, Siegfried M, Yuan YP, Bork P, Lehväslaiho H, Brookes AJ. HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources. Nucleic Acids Res. 2002 Jan 1;30(1):387-91. PubMed PMID: 11752345.
| 2002 | 100 |
Online. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 244 |
HLungDBhttp://www.megabionet.org/bio/hlung |
Incorporates information on the transcription factor binding motifs, the promoters, the SNP sites for each genes, as well as related clinical information and experiment evidences in context to lung cancer. | Wang L, Xiong Y, Sun Y, Fang Z, Li L, Ji H, Shi T. HLungDB: an integrated database of human lung cancer research. Nucleic Acids Res. 2010 Jan;38(Database issue):D665-9. Epub 2009 Nov 9. PubMed PMID: 19900972.
| 2010 | 100 |
URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 245 |
HSPVdb - Human Short Peptide Variation Databasehttp://srs.bioinformatics.nl/hspv/ |
1) Provides information on peptide variation arising due single nucleotide polymorphisms (SNPs). 2) Constructed mainly with the purpose of finding human T cell epitopes and identifying minor histocompatibility antigens (mHags) in combination with mass spectrometry. | Nijveen H, Kester MG, Hassan C, Viars A, de Ru AH, de Jager M, Falkenburg JH, Leunissen JA, van Veelen PA. HSPVdb--the Human Short Peptide Variation Database for improved mass spectrometry-based detection of polymorphic HLA-ligands. Immunogenetics. 2011 Mar;63(3):143-53. Epub 2010 Dec 2. PubMed PMID: 21125265.
| 2011 | 100 |
Online |
| 246 |
IVDB - Influenza Virus Databasehttp://influenza.big.ac.cn/ |
Provides a series of tools and viewers for analyzing the viral genomes, genes, genetic polymorphisms and phylogenetic relationships comparatively. Also, presents the results by SNP distribution plots and minor allele distributions. | Chang S, Zhang J, Liao X, Zhu X, Wang D, Zhu J, Feng T, Zhu B, Gao GF, Wang J, Yang H, Yu J, Wang J. Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research. Nucleic Acids Res. 2007 Jan;35(Database issue):D376-80. Epub 2006 Oct 25. PubMed PMID: 17065465.
| 2007 | 100 |
Online. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 247 |
JSNP - Japanese Single Nucleotide Polymorphismshttp://snp.ims.u-tokyo.ac.jp/ |
Detailed information on the variations in the Japanese population | Hirakawa M, Tanaka T, Hashimoto Y, Kuroda M, Takagi T, Nakamura Y. JSNP: a database of common gene variations in the Japanese population. Nucleic Acids Res. 2002 Jan 1;30(1):158-62. PubMed PMID: 11752280.
| 2002 | 100 |
Online. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 248 |
KAIKObasehttp://sgp.dna.affrc.go.jp/KAIKObase/index.html?keyword-and-position-search |
An integrated silkworm genome database and can provide information on the SNP markers. | Shimomura M, Minami H, Suetsugu Y, Ohyanagi H, Satoh C, Antonio B, Nagamura Y, Kadono-Okuda K, Kajiwara H, Sezutsu H, Nagaraju J, Goldsmith MR, Xia Q, Yamamoto K, Mita K. KAIKObase: an integrated silkworm genome database and data mining tool. BMC Genomics. 2009 Oct 21;10:486. PubMed PMID: 19843344.
| 2009 | 100 |
Online |
| 249 |
LSMDB - Locus Specific Mutation Databaseshttp://www.genomic.unimelb.edu.au/mdi/dblist/glsdb.html |
| Claustres M, Horaitis O, Vanevski M, Cotton RG. Time for a unified system of mutation description and reporting: a review of locus-specific mutation databases. Genome Res. 2002 May;12(5):680-8. PMID:11997335
| 2002 | 100 |
Online. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 250 |
MamPolhttp://mampol.uab.es/ |
Provides information on all the existing polymorphic sequences in the Mammalia group. | Egea R, Casillas S, Fernández E, Senar MA, Barbadilla A. MamPol: a database of nucleotide polymorphism in the Mammalia class. Nucleic Acids Res. 2007 Jan;35(Database issue):D624-9. Epub 2006 Nov 16. PMID:17142236
| 2007 | 100 |
Online. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 251 |
MamuSNPhttp://mamusnp.ucdavis.edu/query.php |
Identifies SNPs, which are widely distributed throughout the coding and non-coding regions of a Macaca mulatta genome. | Malhi RS, Sickler B, Lin D, Satkoski J, Tito RY, George D, Kanthaswamy S, Smith DG. MamuSNP: a resource for Rhesus Macaque (Macaca mulatta) genomics. PLoS One. 2007 May 9;2(5):e438. PubMed PMID: 17487284.
| 2007 | 100 |
Freely downloadable. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 252 |
miRGen 2.0http://diana.cslab.ece.ntua.gr/mirgen/ |
Provides information about the position of human and mouse microRNA coding transcripts and also details on the Single nucleotide polymorphisms associated with microRNAs. | Alexiou P, Vergoulis T, Gleditzsch M, Prekas G, Dalamagas T, Megraw M, Grosse I, Sellis T, Hatzigeorgiou AG. miRGen 2.0: a database of microRNA genomic information and regulation. Nucleic Acids Res. 2010 Jan;38(Database issue):D137-41. Epub 2009 Oct 22. PubMed PMID: 19850714.
| 2010 | 100 |
Online. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 253 |
MitoVariomehttp://variome.kobic.re.kr/MitoVariome/ |
Provides information on the genetic variation in the human mitochondrial genome along with graphical view. | Lee YS, Kim WY, Ji M, Kim JH, Bhak J. MitoVariome: a variome database of human mitochondrial DNA. BMC Genomics. 2009 Dec 3;10 Suppl 3:S12. PMID:19958475
| 2009 | 100 |
Online. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 254 |
MODBASEhttp://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi |
A relational database of annotated comparative protein structure models and also provides information on single nucleotide polymorphisms. | Pieper U, Eswar N, Webb BM, Eramian D, Kelly L, Barkan DT, Carter H, Mankoo P, Karchin R, Marti-Renom MA, Davis FP, Sali A. MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 2009 Jan;37(Database issue):D347-54. Epub 2008 Oct 23. PubMed PMID: 18948282.
| 2009 | 100 |
Online |
| 255 |
MonkeySNPhttp://monkeysnp.ohsu.edu/snp/ OR http://monkeysnp.ohsu.edu/snp/index.jsp |
| Khouangsathiene S, Pearson C, Street S, Ferguson B, Dubay C. MonkeySNP: a web portal for non-human primate single nucleotide polymorphisms. Bioinformatics. 2008 Nov 15;24(22):2645-6. Epub 2008 Sep 16. PubMed PMID: 18796476
| 2008 | 100 |
Online. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 256 |
MutDBhttp://mutdb.org/ |
Annotates human variation data with protein structural and other functionally relevant information. | Singh A, Olowoyeye A, Baenziger PH, Dantzer J, Kann MG, Radivojac P, Heiland R, Mooney SD. MutDB: update on development of tools for the biochemical analysis of genetic variation. Nucleic Acids Res. 2008 Jan;36(Database issue):D815-9. Epub 2007 Sep 7. PubMed PMID: 17827212.
| 2008 | 100 |
Online |
| 257 |
NordicDBhttp://www.nordicdb.org/database/Home.html |
Provides information about the genome-wide association study (GWAS) data samples and details on how to access both the directly genotyped and imputed data. | Leu M, Humphreys K, Surakka I, Rehnberg E, Muilu J, Rosenstrom P, Almgren P, Jaaskelainen J, Lifton RP, Kyvik KO, Kaprio J, Pedersen NL, Palotie A, Hall P, Gronberg H, Groop L, Peltonen L, Palmgren J, Ripatti S. NordicDB: a Nordic pool and portal for genome-wide control data. Eur J Hum Genet. 2010 Dec;18(12):1322-6. Epub 2010 Jul 28. PubMed PMID: 20664631.
| 2010 | 100 |
Data can be downloaded. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 258 |
ORFDBhttp://orf.invitrogen.com/ |
Provides a highly flexible technology (SNP genotyping assays kits) for detection of polymorphism within any genome. | Liang F, Matrubutham U, Parvizi B, Yen J, Duan D, Mirchandani J, Hashima S, Nguyen U, Ubil E, Loewenheim J, Yu X, Sipes S, Williams W, Wang L, Bennett R, Carrino J. ORFDB: an information resource linking scientific content to a high-quality Open Reading Frame (ORF) collection. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D595-9. PubMed PMID: 14681490.
| 2004 | 100 |
Online. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 259 |
Patrocleshttp://www.patrocles.org/MyPatrocles.php |
| Hiard S, Charlier C, Coppieters W, Georges M, Baurain D. Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates. Nucleic Acids Res. 2010 Jan;38(Database issue):D640-51. Epub 2009 Nov 11. PubMed PMID: 19906729.
| 2010 | 100 |
Online. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 260 |
PDA - Pooled DNA Analyzerhttp://www.ibms.sinica.edu.tw/%7Ecsjfann/first%20flow/pda.htm |
Software for the anlysis of pooled DNA data for association studies to identify disease susceptibility genes. | Yang HC, Pan CC, Lin CY, Fann CS. PDA: Pooled DNA analyzer. BMC Bioinformatics. 2006 Apr 28;7:233. PubMed PMID: 16643673.
| 2006 | 100 |
Online. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 261 |
PEPPI - PEPtidomics Protein Isoform Databasehttp://discern.uits.iu.edu:8340/peppi/index.php |
Information on SNPs within the protein isoforms. | Zhou A, Zhang F, Chen JY. PEPPI: a peptidomic database of human protein isoforms for proteomics experiments. BMC Bioinformatics. 2010 Oct 7;11 Suppl 6:S7. PubMed PMID: 20946618.
| 2010 | 100 |
Online URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 262 |
PmiRKBhttp://bis.zju.edu.cn/pmirkb/ |
Detects SNPs in the pre-miRNAs and miRNAs of two model plants- Arabidopsis and Rice. | Meng Y, Gou L, Chen D, Mao C, Jin Y, Wu P, Chen M. PmiRKB: a plant microRNA knowledge base. Nucleic Acids Res. 2011 Jan;39(Database issue):D181-7. Epub 2010 Aug 18. PubMed PMID: 20719744.
| 2011 | 100 |
Online. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 263 |
PoMaMo - Potato Maps and More databasehttp://www.gabipd.org/projects/Pomamo/ |
Provides information on sequences, mapping, SNPs etc. of potato plant. | Meyer S, Nagel A, Gebhardt C. PoMaMo--a comprehensive database for potato genome data. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D666-70. PubMed PMID: 15608284.
| 2005 | 100 |
Online |
| 264 |
Rice DNA polymorphism databasehttp://shenghuan.shnu.edu.cn/ricemarker |
| Shen YJ, Jiang H, Jin JP, Zhang ZB, Xi B, He YY, Wang G, Wang C, Qian L, Li X, Yu QB, Liu HJ, Chen DH, Gao JH, Huang H, Shi TL, Yang ZN. Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol. 2004 Jul;135(3):1198-205. PubMed PMID: 15266053.
| 2004 | 100 |
URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 265 |
rSNP_Guidehttp://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/ |
1) Comprises of 4 sub-databases cross-linked to each other (rSNP_DB, rSNP_BIB, SYSTEM and rSNP_Report. 2) Documents the influence of SNPs in the regulatory gene regions and onto DNA interactions with nuclear proteins. | Ponomarenko JV, Merkulova TI, Orlova GV, Fokin ON, Gorshkova EV, Frolov AS, Valuev VP, Ponomarenko MP. rSNP_Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation. Nucleic Acids Res. 2003 Jan 1;31(1):118-21. PubMed PMID: 12519962.
| 2003 | 100 |
Online |
| 266 |
SNP Function Portalhttp://brainarray.mbni.med.umich.edu/Brainarray/Database/SearchSNP/ snpfunc.aspx |
Provides SNP functional annotations in six major categories including genomic elements, transcription regulation, protein function, pathway, disease and population genetics. | Wang P, Dai M, Xuan W, McEachin RC, Jackson AU, Scott LJ, Athey B, Watson SJ, Meng F. SNP Function Portal: a web database for exploring the function implication of SNP alleles. Bioinformatics. 2006 Jul 15;22(14):e523-9. PubMed PMID: 16873516.
| 2006 | 100 |
Online. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 267 |
SNP resource for Rice http://www.plantgenome.uga.edu/snp |
Information on SNPs of Rice subspecies indica and japonica | Feltus FA, Wan J, Schulze SR, Estill JC, Jiang N, Paterson AH. An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res. 2004 Sep;14(9):1812-9. PubMed PMID: 15342564.
| 2004 | 100 |
URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 268 |
SNPeffecthttp://snpeffect.vib.be/ |
Focuses on the annotation of disease and polymorphism variants present in the human proteome. | Reumers J, Maurer-Stroh S, Schymkowitz J, Rousseau F. SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs. Bioinformatics. 2006 Sep 1;22(17):2183-5. Epub 2006 Jun 29. PubMed PMID: 16809394.
| 2006 | 100 |
Online. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 269 |
SNPExpresshttp://www.planetmathematics.com/SNPExpress/ |
Provides an integrated view of both large scale SNP genotyping and gene expression. | Sanders MA, Verhaak RG, Geertsma-Kleinekoort WM, Abbas S, Horsman S, van der Spek PJ, Löwenberg B, Valk PJ. SNPExpress: integrated visualization of genome-wide genotypes, copy numbers and gene expression levels. BMC Genomics. 2008 Jan 25;9:41. PubMed PMID: 18221515.
| 2008 | 100 |
Freely downloadable. A computer with a memory of 1024MB is advised and it requires a runtime environment of JAVA 1.5 or higher. URL not working (as on 12 Dec 2023) |
| 270 |
SNPperhttp://snpper.chip.org/ |
Retrieves known human SNPs by position or by association with a gene. | Riva A, Kohane IS. SNPper: retrieval and analysis of human SNPs. Bioinformatics. 2002 Dec;18(12):1681-5. PubMed PMID: 12490454.
| 2002 | 100 |
Online registration. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 271 |
SNPSTRhttp://www.sbg.bio.ic.ac.uk/~ino/ |
Information on compound genetic marker called SNPSTR which combines a microsatellite marker (STR) with one or more tightly linked SNPs and severs a great tool to study population genetics of all model organisms. | Agrafioti I, Stumpf MP. SNPSTR: a database of compound microsatellite-SNP markers. Nucleic Acids Res. 2007 Jan;35(Database issue):D71-5. PubMed PMID: 17202172.
| 2007 | 100 |
Online. Displays message "internal error encountered" when tested in Dec 2023 |
| 272 |
SPSmarthttp://spsmart.cesga.es/ |
Provides information on population based SNP data. | Amigo J, Salas A, Phillips C, Carracedo A. SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access. BMC Bioinformatics. 2008 Oct 10;9:428. PubMed PMID: 18847484.
| 2008 | 100 |
Files for execution available |
| 273 |
ssSNPTargethttp://variome.kobic.re.kr/ ssSNPTarget/ or http://ssSNPTarget.org |
Identifies splice-site SNPs distributed in human and mouse genes and their effects on transcripts and mouse. | Yang JO, Kim WY, Bhak J. ssSNPTarget: genome-wide splice-site Single Nucleotide Polymorphism database. Hum Mutat. 2009 Dec;30(12):E1010-20. PubMed PMID: 19760752.
| 2009 | 100 |
URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 274 |
T2D-Dbhttp://t2ddb.ibab.ac.in/home.shtml |
Provides SNP data for the candidate genes reported to be associated with Type2 diabetes. | Agrawal S, Dimitrova N, Nathan P, Udayakumar K, Lakshmi SS, Sriram S, Manjusha N, Sengupta U. T2D-Db: an integrated platform to study the molecular basis of Type 2 diabetes. BMC Genomics. 2008 Jul 7;9:320. PubMed PMID: 18605991.
| 2008 | 100 |
Online. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 275 |
TAMALhttp://neoref.ils.unc.edu/tamal/ |
Provides information on SNPs for genetic studies of human complex traits. | Hemminger BM, Saelim B, Sullivan PF. TAMAL: an integrated approach to choosing SNPs for genetic studies of human complex traits. Bioinformatics. 2006 Mar 1;22(5):626-7. Epub 2006 Jan 17. PubMed PMID: 16418238.
| 2006 | 100 |
Online. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 276 |
TcSNPhttp://snps.tcruzi.org/ |
Provides information on the genetic variation of different strains of Trypanosoma cruzi | Ackermann AA, Carmona SJ, Agüero F. TcSNP: a database of genetic variation in Trypanosoma cruzi. Nucleic Acids Res. 2009 Jan;37(Database issue):D544-9. Epub 2008 Oct 30. PubMed PMID: 18974180.
| 2009 | 100 |
Online. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 277 |
The Bovine Genome Databasehttp://genomes.arc.georgetown.edu/bovine/index.shtml |
| Childers CP, Reese JT, Sundaram JP, Vile DC, Dickens CM, Childs KL, Salih H, Bennett AK, Hagen DE, Adelson DL, Elsik CG. Bovine Genome Database: integrated tools for genome annotation and discovery. Nucleic Acids Res. 2011 Jan;39(Database issue):D830-4. Epub 2010 Dec 1. PubMed PMID: 21123190.
| 2011 | 100 |
Online. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 278 |
The catfish genome database cBARBELhttp://catfishgenome.org/cbarbel/ |
Provides visualization of catfish linkage, physical and integrated maps, a catfish EST contig viewer with SNP information overlay. | Lu J, Peatman E, Yang Q, Wang S, Hu Z, Reecy J, Kucuktas H, Liu Z. The catfish genome database cBARBEL: an informatic platform for genome biology of ictalurid catfish. Nucleic Acids Res. 2011 Jan;39(Database issue):D815-21. Epub 2010 Oct 8. PubMed PMID: 20935046.
| 2011 | 100 |
Online. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 279 |
Definitive Haplotype Database (D-HaploDB)http://orca.gen.kyushu-u.ac.jp/ |
Provides information on genome-wide definitive haplotypes, which are determined by genotyping complete hydatidiform mole samples from Japanese population. | Higasa K, Miyatake K, Kukita Y, Tahira T, Hayashi K. D-HaploDB: a database of definitive haplotypes determined by genotyping complete hydatidiform mole samples. Nucleic Acids Res. 2007 Jan;35(Database issue):D685-9. Epub 2006 Dec 13. PubMed PMID: 17166862.
| 2007 | 100 |
Online. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 280 |
TOMATOMAhttp://tomatoma.nbrp.jp/index.jsp |
Provides information on the mutant seeds of tomato, which are generated by EMS treatment of gamma-ray irradiation. | TOMATOMA: a novel tomato mutant database distributing Micro-Tom mutant collections. Saito T, Ariizumi T, Okabe Y, Asamizu E, Hiwasa-Tanase K, Fukuda N, Mizoguchi T, Yamazaki Y, Aoki K, Ezura H. Plant Cell Physiol. 2011 Feb;52(2):283-96. Epub 2011 Jan 21.
| 2011 | 100 |
Online |
| 281 |
topoSNPhttp://gila.bioengr.uic.edu/snp/toposnp/ |
Provides information about the topographic mapping of the disease and non-disease associated non-synonymous SNPs. | Stitziel NO, Binkowski TA, Tseng YY, Kasif S, Liang J. topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D520-2. PubMed PMID: 14681472.
| 2004 | 100 |
Online. Requires freely available CHIME plug-in for 3D representation of the molecules. URL not working (as on 12 Dec 2023) |
| 282 |
ToxoDBhttp://toxodb.org/toxo/ |
| Gajria B, Bahl A, Brestelli J, Dommer J, Fischer S, Gao X, Heiges M, Iodice J, Kissinger JC, Mackey AJ, Pinney DF, Roos DS, Stoeckert CJ Jr, Wang H, Brunk BP. ToxoDB: an integrated Toxoplasma gondii database resource. Nucleic Acids Res. 2008 Jan;36(Database issue):D553-6. Epub 2007 Nov 14. PubMed PMID: 18003657.
| 2008 | 100 |
Online. Site opens in Mozilla but is not accessible through IE (as on 7 Oct 2013) |
| 283 |
Varietashttp://kokki.uku.fi/bioinformatics/varietas/ |
| Paananen J, Ciszek R, Wong G. Varietas: a functional variation database portal. Database (Oxford). 2010 Jul 29;2010:baq016. Print 2010. PubMed PMID: 20671203.
| 2010 | 100 |
URL not working (as on14 Sep 2013); confirmed in Feb 2017 and Dec 2023 |
| 284 |
VarySysDBhttp://h-invitational.jp/varygene/ |
Comprises of three systems- Genome browser, LD search and VaryGene2 | VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts. Shimada MK, Matsumoto R, Hayakawa Y, Sanbonmatsu R, Gough C, Yamaguchi-Kabata Y, Yamasaki C, Imanishi T, Gojobori T. Nucleic Acids Res. 2009 Jan;37(Database issue):D810-5.
| 2009 | 100 |
Online |
| 285 |
VSDwww.chgb.org.cn/vsd.htm |
1. Provides information on the varitation data, which is extracted from the publicly available databases. 2. Developed as a locus-specific resource to identify susceptible genes for shizophrenia. | Zhou M, Zhuang YL, Xu Q, Li YD, Shen Y. VSD: a database for schizophrenia candidate genes focusing on variations. Hum Mutat. 2004 Jan;23(1):1-7. PubMed PMID: 14695526.
| 2004 | 100 |
URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 286 |
ThaiSNP-2http://www4a.biotec.or.th/thaisnp2/ |
1) Uses the 5th generation Affymetrix SNP genotyping array to determine Single Nucleotide Polymorphisms (SNPs) and Copy Number Variations (CNVs) in Thai population. 2) It can search SNP information from gene, chromosome position, associated disease and SNP ID. | | Not available | 100 |
URL not working (as on 20 Feb 2017); shows default backend confirmed in Dec 2023 |
| 287 |
IGVdbhttp://www.igvdb.res.in/index.php |
1) Aims to discover SNPs, CNVs and repeats in over 1000 genes, which are biomedically important and also genes of pharmacogenetic relevance in the Indian population. 2) Use the haplotype maps for disease association studies and pharmacogenetics. | Indian Genome Variation Consortium. The Indian Genome Variation database (IGVdb): a project overview. Hum Genet. 2005 Oct;118(1):1-11. Epub 2005 Aug 25. Review. PubMed PMID: 16133172
| 2005 | 100 |
Requires online registration. |
| 288 |
HSDB- Horse Single Nucleotide Polymorphism and Expression Databasehttp://snugenome2.snu.ac.kr/HSDB |
Provides information on the SNPs and expression data of the thoroughbred horse population by using NGS data. Has identified 3,148 SNPs in the horse genes. | Lee JH, Lee T, Lee HK, Cho BW, Shin DH, Do KT, Sung S, Kwak W, Kim HJ, Kim H, Cho S, Park KD. Thoroughbred Horse Single Nucleotide Polymorphism and Expression Database: HSDB. Asian-Australas J Anim Sci. 2014 Sep;27(9):1236-43. doi: 10.5713/ajas.2013.13694. PubMed PMID: 25178365; PubMed Central PMCID: PMC4150188.
| 2014 | 100 |
URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 289 |
SNP@lincTFBShttp://bioinfo.hrbmu.edu.cn/SNP_lincTFBS |
Provides information on the (i) disease-associated SNPs present in the human lincRNA TFBSs and SNPs in the TFBSs of disease-associated lincRNAs (ii) phenotype-associated SNPs in lincRNA TFBSs based on GWAS and their annotation (iii) experimentally supported disease associated lincRNAs and SNPs annotation. | Ning S, Zhao Z, Ye J, Wang P, Zhi H, Li R, Wang T, Wang J, Wang L, Li X. SNP@lincTFBS: an integrated database of polymorphisms in human LincRNA transcription factor binding sites. PLoS One. 2014 Jul 30;9(7):e103851. doi: 10.1371/journal.pone.0103851. eCollection 2014. PubMed PMID: 25075616; PubMed Central PMCID: PMC4116217
| 2014 | 100 |
The database can be searched with lincRNA ID, SNP ID and TF name. URL not working (as on 29 Oct 2013); confirmed in Feb 2017 and Dec 2023 |
| 290 |
SInChttp://sourceforge.net/projects/sincsimulator |
A user-friendly multi-variant simulator and read generator, which can simulate all the three common types of variations (Single Nucleotide Polymorphisms, Insertions and Deletions and Copy Number Variations) from the commonly used next-generation sequencing instrument from Illumina. | Pattnaik S, Gupta S, Rao AA, Panda B. SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data. BMC Bioinformatics. 2014 Feb 5;15:40. doi: 10.1186/1471-2105-15-40. PubMed PMID: 24495296; PubMed Central PMCID: PMC3926339
| Not available | 100 |
|
| 291 |
fcGENEhttp://sourceforge.net/projects/fcgene/ |
1) A free open-source format converting tool for genotype SNP data. 2) It transforms SNP data and imputation results into different formats, which is essential for a large variety of analysis packages such as PLINK, SNPTEST, HAPLOVIEW, etc. 3) Performs various data management tasks like merging, splitting, extracting SNP and pedigree information. | Roshyara NR, Scholz M. fcGENE: a versatile tool for processing and transforming SNP datasets. PLoS One. 2014 Jul 22;9(7):e97589. doi: 10.1371/journal.pone.0097589. eCollection 2014. PubMed PMID: 25050709; PubMed Central PMCID: PMC4106754
| 2014 | 100 |
Developed in C++ object-oriented programming language. Downloadable. |
| 292 |
GACT- Genome build and Allele definition Conversion Toolhttp://www.uvm.edu/genomics/software/gact |
Predicts and inter-converts between any of the common SNP allele definitions and between genome builds for genome-wide meta-analysis and imputation of genotypes from SNP-arrays. | Sulovari A, Li D. GACT: a Genome build and Allele definition Conversion Tool for SNP imputation and meta-analysis in genetic association studies. BMC Genomics. 2014 Jul 19;15:610. doi: 10.1186/1471-2164-15-610. PubMed PMID: 25038819
| 2014 | 100 |
Online software. URL not working (as on 12 Dec 2023) |
| 293 |
LincSNPhttp://bioinfo.hrbmu.edu.cn/LincSNP |
1) An integrated database, which identifies and annotates disease-associated SNPs present in the human large intergenic non-coding RNAs (lincRNAs). 2) The current release of LincSNP contains approximately 140,000 disease-associated SNPs (or linkage disequilibrium SNPs), which can be mapped to around 5,000 human lincRNAs. 3) Provides an option for the submission of novel identified SNP-lincRNA-disease associations. | Ning S, Zhao Z, Ye J, Wang P, Zhi H, Li R, Wang T, Li X. LincSNP: a database of linking disease-associated SNPs to human large intergenic non-coding RNAs. BMC Bioinformatics. 2014 May 20;15:152. doi: 10.1186/1471-2105-15-152. PubMed PMID: 24885522; PubMed Central PMCID: PMC4038069
| 2014 | 100 |
Database can be queried by disease/phenotype name, SNP ID, lincRNA name and chromosome region. URL not working (as on 12 Dec 2023) |
| 294 |
mrSNPhttp://mrsnp.osu.edu |
Predicts the effect of a SNP in 3' UTR on miRNA binding. | Deveci M, Catalyürek UV, Toland AE. mrSNP: software to detect SNP effects on microRNA binding. BMC Bioinformatics. 2014 Mar 15;15:73. doi: 10.1186/1471-2105-15-73. PubMed PMID: 24629096; PubMed Central PMCID: PMC4067983
| 2014 | 100 |
URL not working (as on 12 Dec 2023) |
| 295 |
Rice SNP-Seek Databasehttp://www.oryzasnp.org/iric-portal/ |
Provides information on rice SNPs by aligning reads from 3000 rice genomes project with the Nipponbare genome. | Alexandrov N, Tai S, Wang W, Mansueto L, Palis K, Fuentes RR, Ulat VJ, Chebotarov D, Zhang G, Li Z, Mauleon R, Hamilton RS, McNally KL. SNP-Seek database of SNPs derived from 3000 rice genomes. Nucleic Acids Res. 2014 Nov 27. pii: gku1039. [Epub ahead of print] PubMed PMID: 25429973.
| 2014 | 100 |
SNPs can be visualized along with the gene structures in JBrowse genome browser. |
| 296 |
DoGSDhttp://dogsd.big.ac.cn |
1) Provides non-redundant dataset on whole genome SNP data from domesticated dogs and grey wolves. 2) Contains detailed information of each SNP, like, original sample, sequencing platform, chromosome position, SNP annotation, 3/5 flanking sequences, SNPs of same position but detected in other samples, allele frequencies of dog/wolf populations and Fst value between dog and wolf populations. | Bai B, Zhao WM, Tang BX, Wang YQ, Wang L, Zhang Z, Yang HC, Liu YH, Zhu JW, Irwin DM, Wang GD, Zhang YP. DoGSD: the dog and wolf genome SNP database. Nucleic Acids Res. 2014 Nov 17. pii: gku1174. [Epub ahead of print] PubMed PMID: 25404132.
| 2014 | 100 |
The current version contains 19 millions non-redundant SNPs retrived from dbSNP (ver 139) and called from 77 individual smaples. |
| 297 |
VCS- Visualization of Copy number variation and Single nucleotide polymorphismhttp://snugenome.snu.ac.kr/Software/VCS/ |
Provides six visualization tools: i) the enrichment of genome contents in CNV; ii) the physical distribution of CNV or SNP on chromosomes; iii) the distribution of log2 ratio of CNVs; iv) the number of CNV or SNP per binning unit; v) the distribution of homozygosity of SNP genotype; and vi) cytomap of genes within CNV or SNP region. | Kim H, Sung S, Cho S, Kim TH, Seo K, Kim H. VCS: Tool for Visualizing Copy Number Variation and Single Nucleotide Polymorphism. Asian-Australas J Anim Sci. 2014 Dec;27(12):1691-4. doi: 10.5713/ajas.2014.14143. PubMed PMID: 25358361; PubMed Central PMCID: PMC4213679.
| 2014 | 100 |
URL not working (as on 12 Dec 2023) |
| 298 |
lncRNASNPhttp://bioinfo.life.hust.edu.cn/lncRNASNP/ |
1) Provides a comprehensive list of single nucleotide polymorphisms (SNPs) present in human/mouse lncRNAs, and information on the effect of SNPs on lncRNA structure and lncRNA:miRNA binding. 2) LncRNASNP also integrates GWAS data and miRNA expression data into functional SNP selection for genetic association studies. | Gong J, Liu W, Zhang J, Miao X, Guo AY. lncRNASNP: a database of SNPs in lncRNAs and their potential functions in human and mouse. Nucleic Acids Res. 2014 Oct 20. pii: gku1000. [Epub ahead of print] PubMed PMID: 25332392.
| 2014 | 100 |
URL not working (as on 12 Dec 2023) |
| 299 |
GRASP v2.0http://apps.nhlbi.nih.gov/Grasp/Overview.aspx |
1) Provides information on the publically available genome-wide association study (GWAS) results and serves as a repository of associations between SNPs and phenotypes. 2) The database can be queried for SNP associations (P ≤ 0.05) with human traits, including methylation and expression quantitative trait loci (QTL) studies. | Eicher JD, Landowski C, Stackhouse B, Sloan A, Chen W, Jensen N, Lien JP, Leslie R, Johnson AD. GRASP v2.0: an update on the Genome-Wide Repository of Associations between SNPs and phenotypes. Nucleic Acids Res. 2015 Jan 28;43(Database issue):D799-804. doi: 10.1093/nar/gku1202. Epub 2014 Nov 26. PubMed PMID: 25428361.
| 2015 | 100 |
|
| 300 |
Divstathttp://www.portugene.com/DivStat.html |
Allows computation of population genetic data and analyzes DNA haplotype sequences encompassing more than a thousand of base pairs. | Soares I, Moleirinho A, Oliveira GN, Amorim A. DivStat: A User-Friendly Tool for Single Nucleotide Polymorphism Analysis of Genomic Diversity. PLoS One. 2015 Mar 10;10(3):e0119851. doi: 10.1371/journal.pone.0119851. eCollection 2015. PubMed PMID: 25756185
| 2015 | 100 |
Freely available to download. |
| 301 |
GenoExphttp://genie.weizmann.ac.il/pubs/GenoExp/ |
1) Predicts the possible efects that SNPs have on the genes and on their cell-specific expression level. 2) Current version can predict results for 232 genes across 14 different cell types. | Manor O, Segal E. GenoExp: a web tool for predicting gene expression levels from single nucleotide polymorphisms. Bioinformatics. 2015 Jan 30. pii: btv050. [Epub ahead of print] PubMed PMID: 25637557.
| 2015 | 100 |
Tool is freely available. Software supports prediction of expression for only one individual; to obtain results for many individuals we need to download the MATLAB code. URL not working (as on 12 Dec 2023) |
| 302 |
Remo-SNPshttp://www.neuro.ki.se/ReMo-SNPs/ |
1) A software tool, which identifies SNPs present in regions and motifs genome-wide. 2) Provides automatic selection of the genotyped markers in the user provided material. | Graae L, Paddock S, Belin AC. ReMo-SNPs: a new software tool for identification of polymorphisms in regions and motifs genome-wide. Genet Res (Camb). 2015 Apr 17;97:e8. doi: 10.1017/S0016672315000051. PubMed PMID: 25882789.
| 2015 | 100 |
Program is written in Perl and requires a Perl interpreter to run the script. Freely downloadable. |
| 303 |
ChroMoS- Chromatin Modified SNPshttp://epicenter.immunbio.mpg.de/services/chromos |
1) Combines genetic and epigenetic data, which assists in the classification of SNPs, their prioritization and prediction of functional consequences. 2) Functional impact of multiple SNPs can be computed by using prediction tools like sTRAR and MicroSNiPer. | Barenboim M, Manke T. ChroMoS: an integrated web tool for SNP classification, prioritization and functional interpretation. Bioinformatics. 2013 Sep 1;29(17):2197-8. doi: 10.1093/bioinformatics/btt356. Epub 2013 Jun 19. PubMed PMID: 23782616; PubMed Central PMCID: PMC3740627.
| 2013 | 100 |
|
| 304 |
miRNASNPhttp://bioinfo.life. hust.edu.cn/miRNASNP2/ |
1) Provides information on SNPs present in miRNA and genes, which effect miRNA biogenesis and miRNA target binding. 2) Version 2 (v2.0) provides an option of multiple filters to prioritize functional SNPs, information on the expression level and expression correlation of miRNAs and target genes in different tissues, link SNPs to the results of genome-wide association studies and integrates experimentally validated miRNA:mRNA interactions. | Gong J, Liu C, Liu W, Wu Y, Ma Z, Chen H, Guo AY. An update of miRNASNP database for better SNP selection by GWAS data, miRNA expression and online tools. Database (Oxford). 2015 Apr 15;2015. pii: bav029. doi: 10.1093/database/bav029. Print 2015. PubMed PMID: 25877638; PubMed Central PMCID: PMC4397995.
| 2015 | 100 |
|
| 305 |
SNePhttps://sourceforge.net/projects/snepnetrends/ |
Uses genome-wide SNP data to estimate the effective population (Ne) size, which can be useful in undestanding population demography when a sufficient number of SNPs and their phhysical position in the genomes is available. | Barbato M, Orozco-terWengel P, Tapio M, Bruford MW. SNeP: a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data. Front Genet. 2015 Mar 20;6:109. doi: 10.3389/fgene.2015.00109. eCollection 2015. PubMed PMID: 25852748; PubMed Central PMCID: PMC4367434.
| 2015 | 100 |
|
| 306 |
SNPsnaphttp://www.broadinstitute.org/mpg/snpsnap/ |
1) Allows identification and annotation of matched SNPs based on based on allele frequency, number of SNPs in LD, distance to nearest gene and gene density. 2) X-chromosome SNPs and Super populations (European, EUR; East Asian, EAS; West African, WAFR) are included to allow more specific SNP matching based on your study population. | Pers TH, Timshel P, Hirschhorn JN. SNPsnap: a Web-based tool for identification and annotation of matched SNPs. Bioinformatics. 2015 Feb 1;31(3):418-20. doi: 10.1093/bioinformatics/btu655. Epub 2014 Oct 13. PubMed PMID: 25316677; PubMed Central PMCID: PMC4308663.
| 2015 | 100 |
Current release is based on 1000 Genome Phase 3 data and the old phase 1 data is no longer supported. PLINK 1.9 is used for clumping input SNPs. URL not working (as on 12 Dec 2023) |
| 307 |
SITDEMhttp://www.snpmodel.com |
Serves as a simulation tool for disease/endpoint models of association studies based on SNP genotypes and is useful in investigating the relationship among observed parameters for target SNPs. | Oh JH, Deasy JO. SITDEM: a simulation tool for disease/endpoint models of association studies based on single nucleotide polymorphism genotypes. Comput Biol Med. 2014 Feb;45:136-42. doi: 10.1016/j.compbiomed.2013.11.021. Epub 2013 Dec 19. PubMed PMID: 24480173.
| 2014 | 100 |
URL not working (as on 12 Dec 2023) |
| 308 |
PANOGA- Pathway and Network Oriented GWAS (Genome-Wide Association Study) Analysishttp://panoga.sabanciuniv.edu/ |
1) Identifies SNP targeted pathways from genome-wide association study data. 2) Provides information on the regulatory SNPs (SNPs located on TFBSs or miRNAs), the disease predisposing SNPs and number of SNP-targeted genes. | Bakir-Gungor B, Egemen E, Sezerman OU. PANOGA: a web server for identification of SNP-targeted pathways from genome-wide association study data. Bioinformatics. 2014 May 1;30(9):1287-9. doi: 10.1093/bioinformatics/btt743. Epub 2014 Jan 11. PubMed PMID: 24413675.
| 2014 | 100 |
URL not working (as on 17 Feb 2017); confirmed in Dec 2023 |
| 309 |
HapRicehttp://qtaro.abr.affrc.go.jp/index.html |
1) Performs genome-wide SNP analysis and finds the genetic diversity in the rice populations. 2) Provides data on the the allele frequencies of 3,334 SNPs in 76 accessions from the world rice collection and 3,252 SNPs in 177 Japanese rice accessions. | Yonemaru J, Ebana K, Yano M. HapRice, an SNP haplotype database and a web tool for rice. Plant Cell Physiol. 2014 Jan;55(1):e9. doi: 10.1093/pcp/pct188. Epub 2013 Dec 13. PubMed PMID: 24334415
| 2014 | 100 |
The given URL links to Q-TARO (QTL Annotation Rice Online) database. URL not working (as on 12 Dec 2023) |
| 310 |
rSNPBasehttp://rsnp.psych.ac.cn/ |
Provides information on human regulatory SNPs (rSNPs), which are involved in a wide range of regulation types, including proximal and distal transcriptional regulation and post-transcriptional regulation, and identifies their potentially regulated genes. | Guo L, Du Y, Chang S, Zhang K, Wang J. rSNPBase: a database for curated regulatory SNPs. Nucleic Acids Res. 2014 Jan;42(Database issue):D1033-9. doi: 10.1093/nar/gkt1167. Epub 2013 Nov 26. PubMed PMID: 24285297; PubMed Central PMCID: PMC3964952.
| 2014 | 100 |
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| 311 |
TRAMS- Tool for rapid annotation of microbial SNPshttp://sourceforge.net/projects/strathtrams/files/Latest/ |
Provides fast and accurate annotation of SNPs, which is useful in analyzing genomic diversity in the microbial populations | Reumerman RA, Tucker NP, Herron PR, Hoskisson PA, Sangal V. Tool for rapid annotation of microbial SNPs (TRAMS): a simple program for rapid annotation of genomic variation in prokaryotes. Antonie Van Leeuwenhoek. 2013 Sep;104(3):431-4. doi: 10.1007/s10482-013-9953-x. Epub 2013 Jul 5. PubMed PMID: 23828175
| 2013 | 100 |
Can be downloaded as a Python script and single file executable for WINDOWS from the given URL. |
| 312 |
QualitySNPnghttp://www.bioinformatics.nl/QualitySNPng |
1) Detects and provides an interactive visualization of SNPs, and uses a haplotype-based strategy to identify reliable SNPs. 2) Suitable for the analysis of current RNA-seq data; but it can also be used on genomic DNA sequences derived from next-generation sequencing experiments. | Nijveen H, van Kaauwen M, Esselink DG, Hoegen B, Vosman B. QualitySNPng: a user-friendly SNP detection and visualization tool. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W587-90. doi: 10.1093/nar/gkt333. Epub 2013 Apr 30. PubMed PMID: 23632165; PubMed Central PMCID: PMC3692117
| 2013 | 100 |
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| 313 |
RNAsnphttp://rth.dk/resources/rnasnp/ |
1) Predicts the effect of SNPs on local RNA secondary structure based on the RNA folding algorithms implemented in the Vienna RNA package. 2) Additionally, allows the users to select the genomic sequences for analysis and visualize the results directly in the UCSC genome browser. | Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J. The RNAsnp web server: predicting SNP effects on local RNA secondary structure. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W475-9. doi: 10.1093/nar/gkt291. Epub 2013 Apr 29. PubMed PMID: 23630321; PubMed Central PMCID: PMC3977658
| 2013 | 100 |
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| 314 |
SNPranker 2.0http://www.itb.cnr.it/snpranker |
Serves as a data mining tool for disease associated SNPs and provides information on GWAS data re-scoring, SNPs selection for custom genotyping arrays and SNPs/diseases association studies. | Merelli I, Calabria A, Cozzi P, Viti F, Mosca E, Milanesi L. SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS. BMC Bioinformatics. 2013;14 Suppl 1:S9. doi: 10.1186/1471-2105-14-S1-S9. Epub 2013 Jan 14. PubMed PMID: 23369106; PubMed Central PMCID: PMC3548692.
| 2013 | 100 |
URL not working (as on 12 Dec 2023) |
| 315 |
snpTreehttp://www.cbs.dtu.dk/services/snpTree-1.0/ |
Performs online-automatic SNP analysis by identifying SNPs and constructructing phylogenetic trees from WGS as well as from assembled genomes or contigs. | Leekitcharoenphon P, Kaas RS, Thomsen MC, Friis C, Rasmussen S, Aarestrup FM. snpTree--a web-server to identify and construct SNP trees from whole genome sequence data. BMC Genomics. 2012;13 Suppl 7:S6. doi: 10.1186/1471-2164-13-S7-S6. Epub 2012 Dec 13. PubMed PMID: 23281601; PubMed Central PMCID: PMC3521233
| 2012 | 100 |
URL not working (as on 12 Dec 2023) |
| 316 |
SYSNPs http://www.sysnps.org/ |
1) Allows the user to compile information about all the SNPs in any human gene or genome region of interest. 2) Select the SNPs based on different criteria, such as functional properties, technological information and tagging information from their choice populations. | Lorente-Galdos B, Medina I, Morcillo-Suarez C, Heredia T, Carreño-Torres A, Sangrós R, Alegre J, Pita G, Vellalta G, Malats N, Pisano DG, Dopazo J, Navarro A. Select your SNPs (SYSNPs): a web tool for automatic and massive selection of SNPs. Int J Data Min Bioinform. 2012;6(3):324-34. PubMed PMID: 23155765
| 2012 | 100 |
URL not working as on 30 May 2015; confirmed in Feb 2017 and Dec 2023 |
| 317 |
PESNPdb- Pre-eclampsia SNP resourcehttp://bejerano.stanford.edu/pesnpdb |
Identifies SNPs, which contribute towards the genetic susceptibility of pre-eclampsia. | Tuteja G, Cheng E, Papadakis H, Bejerano G. PESNPdb: a comprehensive database of SNPs studied in association with pre-eclampsia. Placenta. 2012 Dec;33(12):1055-7. doi: 10.1016/j.placenta.2012.09.016. Epub 2012 Oct 18. PubMed PMID: 23084601.
| 2012 | 100 |
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| 318 |
CYP-nsSNP http://cypdatabase.sjtu.edu.cn/ |
1) Provides information on the effect of SNPs on the function and enzymatic activity of cytochrome P450 (CYP) enzymes. 2) Includes data on more than 300 genetic variants of 12 CYP isozymes together with about 100 compounds. | Zhang T, Zhou Q, Pang Y, Wang Y, Jin C, Huo J, Liu LA, Wei D. CYP-nsSNP: a specialized database focused on effect of non-synonymous SNPs on function of CYPs. Interdiscip Sci. 2012 Jun;4(2):83-9. doi: 10.1007/s12539-012-0125-x. Epub 2012 Jul 29. PubMed PMID: 22843230
| 2012 | 100 |
URL not working as on 16 June 2015; confirmed in Feb 2017 and Dec 2023 |
| 319 |
AncestrySNPminerhttps://research.cchmc.org/mershalab/AncestrySNPminer/login.php |
Performs population genomics statistical analyses to retrieve SNPs that are informative for ancestry. | Amirisetty S, Hershey GK, Baye TM. AncestrySNPminer: a bioinformatics tool to retrieve and develop ancestry informative SNP panels. Genomics. 2012 Jul;100(1):57-63. doi: 10.1016/j.ygeno.2012.05.003. Epub 2012 May 11. PubMed PMID: 22584067; PubMed Central PMCID: PMC3433799
| 2012 | 100 |
|
| 320 |
LDGIdb- Linkage-Disequilibrium-based Gene Interaction database (LDGIdb)http://LDGIdb.genomics.sinica.edu.tw |
Provides information non-physical SNP linkages and SNP-disease associations, which can be useful for studies of gene interactions in human diseases. Stores more than 2 million human gene interactions. Data from long-range strong linkage disequilibrium between pairs of SNPs either from exonic or promoter region. | Wang MC, Chen FC, Chen YZ, Huang YT, Chuang TJ. LDGIdb: a database of gene interactions inferred from long-range strong linkage disequilibrium between pairs of SNPs. BMC Res Notes. 2012 May 2;5:212. doi: 10.1186/1756-0500-5-212. PubMed PMID: 22551073; PubMed Central PMCID: PMC3441865
| 2012 | 100 |
Online. URL not working as on 16 June 2015; confirmed in Feb 2017 and Dec 2023 |
| 321 |
KAREBrowser: SNP database of Korea Association REsource Projecthttp://ksnp.cdc. go.kr/karebrowser/ |
Provides users with a large amount of single nucleotide polymorphisms (SNPs) information, which comprises of 1.5 million SNPs from population-based cohorts of 8,842 Korean subjects. | Hong CB, Kim YJ, Moon S, Shin YA, Cho YS, Lee JY. KAREBrowser: SNP database of Korea Association REsource Project. BMB Rep. 2012 Jan;45(1):47-50. PubMed PMID: 22281013
| 2012 | 100 |
Website states that the new version will be launched soon. URL not working (as on 19 Feb 2017); confirmed in Dec 2023 |
| 322 |
miRdSNPhttp://mirdsnp.ccr.buffalo.edu |
1) Provides information on important areas of disease-associated SNPs (dSNPs), microRNA target sites on 3'UTRs and diseases. 2) Current release incorporates 786 dSNP-disease associations for 630 unique dSNPs and 204 disease types. | Bruno AE, Li L, Kalabus JL, Pan Y, Yu A, Hu Z. miRdSNP: a database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes. BMC Genomics. 2012 Jan 25;13:44. doi: 10.1186/1471-2164-13-44. PubMed PMID: 22276777; PubMed Central PMCID: PMC3287127
| 2012 | 100 |
URL not working (as on 19 Feb 2017); confirmed in Dec 2023 |
| 323 |
SNPxGE(2)http://lambchop.ads.uga.edu/snpxge2/index.php |
Provides information on the computationally predicted human SNP-coexpression associations, i.e. the differential coexpression between two genes is associated with the genotype of an SNP. | Wang Y, Joseph SJ, Liu X, Kelley M, Rekaya R. SNPxGE(2): a database for human SNP-coexpression associations. Bioinformatics. 2012 Feb 1;28(3):403-10. doi: 10.1093/bioinformatics/btr663. Epub 2011 Nov 30. PubMed PMID: 22135417
| 2012 | 100 |
URL not working (as on 19 Feb 2017); confirmed in Dec 2023 |
| 324 |
NovelSNPerhttp://www2.hu-berlin.de/wikizbnutztier/software/NovelSNPer/ |
Identifies and characterizes novel SNPs and InDels and classifies each variant into one of 15 SNP classes or 19 InDel classes. | Aßmus J, Schmitt AO, Bortfeldt RH, Brockmann GA. NovelSNPer: A Fast Tool for the Identification and Characterization of Novel SNPs and InDels. Adv Bioinformatics. 2011;2011:657341. doi: 10.1155/2011/657341. Epub 2011 Oct 31. PubMed PMID: 22110502; PubMed Central PMCID: PMC3206323
| 2011 | 100 |
Tool is available online or can be downloaded. |
| 325 |
Snat- SNP annotation toolhttp://animalgenetics.cau.edu.cn/snat/ |
Captures SNP annotation for livestock and provides a convenient and powerful platform to aid functional analyses and accurate evaluation on genes/variants related to SNPs, and facilitates follow-up replication studies in the post-GWAS era. | Jiang J, Jiang L, Zhou B, Fu W, Liu JF, Zhang Q. Snat: a SNP annotation tool for bovine by integrating various sources of genomic information. BMC Genet. 2011 Oct 7;12:85. doi: 10.1186/1471-2156-12-85. PubMed PMID: 21982513; PubMed Central PMCID: PMC3224132
| 2011 | 100 |
URL not working (as on 19 Feb 2017); confirmed in Dec 2023 |
| 326 |
PanSNPdb-the Pan-Asian SNP genotyping databasehttp://www4a.biotec.or.th/PASNP |
Database having genetic variation data of about 1,719 unrelated individuals among 71 populations from China, India, Indonesia, Japan, Malaysia, the Philippines, Singapore, South Korea, Taiwan, and Thailand. | Ngamphiw C, Assawamakin A, Xu S, Shaw PJ, Yang JO, Ghang H, Bhak J, Liu E, Tongsima S, HUGO Pan-Asian SNP Consortium. PanSNPdb: the Pan-Asian SNP genotyping database. PloS one. 2011 Jun 23;6(6):e21451. PubMed PMID: 21731755
| 2011 | 100 |
Download. URL not working (as on 19 Feb 2017); confirmed in Dec 2023 |
| 327 |
BALL-SNPgphttp://www.ccb.uni-saarland.de/software/ballsnp/?id=www/www-ccb/html/BALL-SNPgp |
1) A tool for structural and functional characterization of non-synonymous single nucleotide variants (nsSNVs). 2) Creates a three-dimensional visualization of the encoded protein, collects available information from different resources concerning disease relevance. | Mueller SC, Backes C, Gress A, Baumgarten N, Kalinina OV, Moll A, Kohlbacher O, Meese E, Keller A. BALL-SNPgp—from genetic variants toward computational diagnostics. Bioinformatics. 2016 Feb 15:btw084. PubMed PMID: 27153685
| 2016 | 100 |
Downloadable |
| 328 |
CsSNP-Comparative segments SNPhttp://biodb.sdau.edu.cn/cssnp/ |
1) Detects comparative segments SNPs through the Blat, Blast and perl programs. 2) Used to show detailed information on SNPs. | Wang Y, Wang S, Zhou D, Yang S, Xu Y, Yang C, Yang L. CsSNP: A Web-Based Tool for the Detecting of Comparative Segments SNPs. J Comput Biol. 2016 Jul;23(7):597-602. doi: 10.1089/cmb.2015.0215. PubMed PMID: 27347883
| 2015 | 100 |
Online. URL not working (as on 19 Feb 2017); confirmed in Dec 2023 |
| 329 |
SNPMetahttp://www.tc.umn.edu/~konox006/Code/SNPMeta/ |
1) Plays role in SNP annotation without having a reference genome 2) Also used for SNP metadata collection | Kono TJ, Seth K, Poland JA, Morrell PL. SNPMeta: SNP annotation and SNP metadata collection without a reference genome. Molecular ecology resources. 2014 Mar 1;14(2):419-25. PubMed PMID: 24237904
| 2014 | 100 |
Online and Downloadable. URL not working (as on 19 Feb 2017); confirmed in Dec 2023 |
| 330 |
SNiPlayhttp://sniplay.southgreen.fr/cgi-bin/home.cgi |
1) Web-based tool, that analyzes genetic variants (SNPs and InDels). 2) Also used for the detection and management of the genetic variants | Dereeper A, Nicolas S, Le Cunff L, Bacilieri R, Doligez A, Peros JP, Ruiz M, This P. SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects. BMC bioinformatics. 2011 May 5;12(1):1. PubMed PMID: 21545712
| 2011 | 100 |
Online |
| 331 |
rVarBaserv.psych.ac.cn |
1) Database updated having the regulatory features of human variants. 2) Used to annotate, variant's regulatory features, basically in three fields viz; chromatin state surrounding variant region, regulatory elements overlapped with variants and the potential target genes of variants. | Guo L, Du Y, Qu S, Wang J. rVarBase: an updated database for regulatory features of human variants. Nucleic Acids Res. 2016 Jan 4;44(D1):D888-93. doi: 10.1093/nar/gkv1107. PubMed PMID: 26503253; PubMed Central PMCID: PMC4702808.
| 2009 | 100 |
Online and Downloadable |
| 332 |
SorGSD- a sorghum genome SNP databasehttp://sorgsd.big.ac.cn/ |
Provides information on genomic variations occuring across all racial types of cultivated sorghum, as well as its wild relatives | Luo H, Zhao W, Wang Y, Xia Y, Wu X, Zhang L, Tang B, Zhu J, Fang L, Du Z, Bekele WA. SorGSD: a sorghum genome SNP database. Biotechnology for biofuels. 2016 Jan 7;9(1):1. PubMed PMID: 26744602
| 2016 | 100 |
Online and Downloadable |
| 333 |
atSNPhttps://github.com/keleslab/atSNP |
Used for testing transcription factor binding affinity for regulatory SNP detection | Zuo C, Shin S, Keleş S. atSNP: transcription factor binding affinity testing for regulatory SNP detection. Bioinformatics. 2015 Jun 18:btv328. PubMed PMID: 26092860
| 2015 | 100 |
Installable as R package |
| 334 |
JEPEGMIXhttp://dleelab.github.io/jepegmix/ |
Statistics based tool used for gene-level joint analysis of functional variants including SNPs | Lee D, Williamson VS, Bigdeli TB, Riley BP, Webb BT, Fanous AH, Kendler KS, Vladimirov VI, Bacanu SA. JEPEGMIX: gene-level joint analysis of functional SNPs in cosmopolitan cohorts. Bioinformatics. 2015 Oct 1:btv567. PubMed PMID: 26428293
| 2015 | 100 |
Downloadable |
| 335 |
SNPhoodhttp://bioconductor.org/packages/SNPhood/ |
Investigates and visualizes the local epigenomic neighbourhood of SNPs using NGS data. | Arnold C, Bhat P, Zaugg JB. SNPhood: investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data. Bioinformatics. 2016 Mar 26:btw127. PubMed PMID: 27153574
| 2016 | 100 |
Installable as R package |
| 336 |
nsSNPAnalyzersnpanalyzer.uthsc.edu |
1) A web-based software developed to extract structural and evolutionary infromation from query nsSNPs, 2) Identifies disease-associated nsSNPs from a large number of neutral nsSNPs | Bao L, Zhou M, Cui Y. nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms. Nucleic acids research. 2005 Jul 1;33(suppl 2):W480-2. PubMed PMID: 15980516
| 2005 | 100 |
Online. URL not working (as on 19 Feb 2017); confirmed in Dec 2023 |
| 337 |
PON-P: the Pathogenic-or-Not-Pipelinestructure.bmc.lu.se/PON-P2/ |
Functional prediction tool, developed by integrating five predictors for predicting the affect of nsSNPs on protein function. | Olatubosun A, Väliaho J, Härkönen J, Thusberg J, Vihinen M. PON‐P: Integrated predictor for pathogenicity of missense variants. Human mutation. 2012 Aug 1;33(8):1166-74. PubMed PMID: 22505138
| 2012 | 100 |
Online |
| 338 |
DisGeNEThttp://www.disgenet.org/web/DisGeNET/menu/search?0 |
1)Integrates, searches and analyzes infromation on gene-disease association. 2) Developed from several public data sources and literature. 3) Contains 429,036 associations (between 17,381) genes & 15,093 diseases) and 72,870 variant disease associations (between 46,589 SNPs & 6,356 diseases). | Bauer-Mehren A, Rautschka M, Sanz F, Furlong LI. DisGeNET: a Cytoscape plugin to visualize, integrate, search and analyze gene–disease networks. Bioinformatics. 2010 Nov 15;26(22):2924-6. PubMed PMID: 20861032
| 2010 | 100 |
Online |
| 339 |
3DSNPhttp://biotech.bmi.ac.cn/3dsnp/ |
Database that links the human non-coding SNPs to their 3D interacting genes by integrating informations on 3D chromatin interactions, local chromatin signatures and Linkage Disequilibrium (LD) from 1000 Genomes Project | Lu Y, Quan C, Chen H, Bo X, Zhang C. 3DSNP: a database for linking human noncoding SNPs to their three-dimensional interacting genes. Nucleic Acids Research. 2016 Oct 26:gkw1022. PubMed PMID: 27789693
| 2016 | 100 |
Online. Upgraded to link- https://www.omic.tech/3dsnp/ https://omic.tech/3dsnpv2/ |
| 340 |
TheSNPpithttps://filemare.com/en-in/browse/192.108.34.54/pub/TheSNPpit |
1) Database system for storage and management of large volumes of SNP data. 2) Stores about 3.4 trillion SNPs in 840GB for the genotype data plus around 9GB for everything else including SNP names and sample IDs. | Groeneveld E, Lichtenberg H. TheSNPpit—A High Performance Database System for Managing Large Scale SNP Data. PloS one. 2016 Oct 25;11(10):e0164043. PubMed PMID: 27780248
| 2016 | 100 |
Downloadable. URL not working (as on 19 Feb 2017); confirmed in Dec 2023 |
| 341 |
SpinachDBhttp://222.73.98.124/spinachdb |
1) Stores, annotates, mines and analyzes genomics and genetics datasets of spinach efficiently. 2) Also contains SNP information of spinach. | Yang XD, Tan HW, Zhu WM. SpinachDB: A well-characterized genomic database for gene family classification and SNP information of spinach. PloS one. 2016 May 5;11(5):e0152706. PubMed PMID: 27148975
| 2016 | 100 |
URL not working (as on 19 Feb 2017); confirmed in Dec 2023 |
| 342 |
DHOEM-Densification of Haplotypes by lOEess and Maximum Likelihoodhttps://sourceforge.net/projects/dhoem/ |
Novel R application which performs simulation of new markers in real SNP marker data. | Jacquin L, Cao TV, Grenier C, Ahmadi N. DHOEM: a statistical simulation software for simulating new markers in real SNP marker data. BMC bioinformatics. 2015 Dec 3;16(1):404. PubMed PMID: 26634451
| 2015 | 100 |
Downloadable |
| 343 |
NABIC SNP-National Agricultural Biotechnology Information Centerhttp://nabic.rda.go.kr/SNP |
1) Web-based database providing information on 54,310 SNPs identified in the seven species in a high-throughput manner. 2) Has three major functional categories: SNP marker search, detailed information viewer and download of SNP sequence | Kim CK, Won SY, Seol YJ, Lee TH. NABIC SNP: an integrated database for SNP markers. Bioinformation. 2015;11(7):369. PubMed PMID: 26339155
| 2015 | 100 |
Online |
| 344 |
CicArVarDBhttp://cicarvardb.icrisat.org/ |
1) Database with a repository of 1.0 million variations (SNPs and InDels) of Chickpea. 2) Used for genetic research and breeding application in Chickpea. | Doddamani D, Khan AW, Katta MA, Agarwal G, Thudi M, Ruperao P, Edwards D, Varshney RK. CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea. Database. 2015 Jan 1;2015:bav078. PubMed PMID: 26289427
| 2015 | 100 |
Online |
| 345 |
SCYPPredhttp://snppred.sjtu.edu.cn |
Web-server developed for predicting human cytochrome P450 SNPs. | Li L, Wei DQ, Wang JF, Chou KC. SCYPPred: a web-based predictor of SNPs for human cytochrome P450. Protein and peptide letters. 2012 Jan 1;19(1):57-61. PubMed PMID: 21919859
| 2012 | 100 |
URL not working (as on 19 Feb 2017); confirmed in Dec 2023 |
| 346 |
CalMaTehttps://cran.r-project.org/web/packages/calmate/index.html |
Calibrates preprocessed allele-specific copy number estimates (ASCNs) from DNA microarrays by controlling for single-nucleotide polymorphism-specific allelic crosstalk. | Ortiz-Estevez M, Aramburu A, Bengtsson H, Neuvial P, Rubio A. CalMaTe: A method and software to improve allele-specific copy number of SNP arrays for downstream segmentation. Bioinformatics. 2012 Jul 1;28(13):1793-4. PubMed PMID: 22576175
| 2012 | 100 |
Downloadable R package |
| 347 |
I-GSEA4GWAS v2http://gsea4gwas-v2.psych.ac.cn/ |
Used for comprehensive GWAS data interpretation, namely functional analysis of SNPs in trait associated pathways identified from genome-wide association study. | Zhang K, Chang S, Guo L, Wang J. I-GSEA4GWAS v2: a web server for functional analysis of SNPs in trait-associated pathways identified from genome-wide association study. Protein & cell. 2015 Mar;6(3):221. PubMed PMID: 25407412
| 2015 | 100 |
Freely available web-server. Temporarily unavailableas on 12 Dec 2023 |
| 348 |
SELEX_DBhttp://wwwmgs.bionet.nsc.ru/mgs/systems/selex/ |
1) Online resource supplemented by two databases, SYSTEM &CROSS_TEST. 2) Used for analyzing both SNPs and site-directed mutagenesis. 3) Contains data on in vitro selected oligomers from recognizing natural sites. | Ponomarenko JV, Orlova GV, Frolov AS, Gelfand MS, Ponomarenko MP. SELEX_DB: a database on in vitro selected oligomers adapted for recognizing natural sites and for analyzing both SNPs and site-directed mutagenesis data. Nucleic acids research. 2002 Jan 1;30(1):195-9. PubMed PMID: 11752291
| 2002 | 100 |
Online |
| 349 |
SNP2NMDhttp://variome.kobic.re.kr/SNP2NMD/ |
1) Contains data on Human SNPs which results in premature termination codons and triggers nonsense-mediated mRNA decay (NMD). 2) Provides extensive genetic information on and graphical views of the queried SNP, gene, and disease terms. | Han A, Kim WY, Park SM. SNP2NMD: a database of human single nucleotide polymorphisms causing nonsense-mediated mRNA decay. Bioinformatics. 2007 Feb 1;23(3):397-9. PubMed PMID: 17121775
| 2007 | 100 |
URL not working (as on 19 Feb 2017); confirmed in Dec 2023 |
| 350 |
FstSNP-HapMap3https://code.google.com/archive/p/fstsnp-hapmap3/ |
1) Provides 115, 212 entries of 28,215 SNPs with high differentiation among 48 different combinations of the HapMap3 samples. 2) Six columns viz; SNP, SNP_CHR, SNP_POSI, Fst value, Tested_Populations and DbSNP129_Class are present. | Duan S, Zhang W, Cox NJ, Dolan ME. FstSNP-HapMap3: a database of SNPs with high population differentiation for HapMap3. Bioinformation. 2008 Jan 1;3(3):139-41. PubMed PMID: 19238253
| 2008 | 100 |
Downloadable. URL not working as on 12 Dec 2023 |
