1 |
CONTRAST - CONditionally TRAined Search for Transcriptshttp://contra.stanford.edu/contrast/ |
Predicts protein-coding genes from a multiple genomic alignment. It is designed for de novo predictions. It can also incorporate information from EST alignments. |
| Gross SS, Do CB, Sirota M, Batzoglou S. CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biol. 2007;8(12):R269. PubMed PMID: 18096039; PubMed Central PMCID: PMC2246271.
|
| 2007 | 1 |
Predicitions downloadable or can be browsed by using UCSC genome browser. Predicitions downloadable or can be browsed by using UCSC genome browser. |
2 |
AgenDA - Alignment based Gene Detection Algorithmhttp://bibiserv.techfak.uni-bielefeld.de/agenda/ |
Gene prediction tool performing searches for conserved splice sites and start/stop codons. It also identifies potential exons. |
| Taher L, Rinner O, Garg S, Sczyrba A, Brudno M, Batzoglou S, Morgenstern B. AGenDA:homology-based gene prediction. Bioinformatics. 2003 Aug
12;19(12):1575-7. PubMed PMID: 12912840. |
| 2003 | 99 |
1) Results are obtained in e-mail 2) Gene information provides Gene number. 3) Provides information about the reading frame (0,1,2) 4) Gives information about the DNA strand, whether + or - 1) Results are obtained in e-mail 2) Gene information provides Gene number. 3) Provides information about the reading frame (0,1,2) 4) Gives information about the DNA strand, whether + or - |
3 |
BLAT - BLAST like Alignment toolhttp://genome.ucsc.edu/cgi-bin/hgBlat?command=start |
| Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002
Apr;12(4):656-64. PubMed PMID: 11932250; PubMed Central PMCID: PMC187518.
|
| 2002 | 99 |
1) Link to UCSC Genome browser is given. 2) Splice Sites are marked in the sequence itself, with light blue colour. 1) Link to UCSC Genome browser is given. 2) Splice Sites are marked in the sequence itself, with light blue colour. |
4 |
C-Ithttp://C-It.mpi-bn.mpg.de |
| Gellert P, Jenniches K, Braun T, UchIDa S. C-It: a knowledge database for tissue-enriched genes. Bioinformatics. 2010 Sep 15;26(18):2328-33. Epub 2010 Jul
13. PubMed PMID: 20628071.
|
| 2010 | 99 |
1) Search results downloadable. 2) Gives links to all the pubmed articles mentioning the queried gene 1) Search results downloadable. 2) Gives links to all the pubmed articles mentioning the queried gene |
5 |
ASAP II - Alternative Splicing Annotation Projecthttp://bioinfo.mbi.ucla.edu/ASAP2/ |
| Kim N, Alekseyenko AV, Roy M, Lee C. The ASAP II database: analysis and
comparative genomics of alternative splicing in 15 animal species. Nucleic AcIDs
Res. 2007 Jan;35(Database issue):D93-8. Epub 2006 Nov 15. PubMed PMID: 17108355;
PubMed Central PMCID: PMC1669709.
|
| 2006 | 100 |
1) Gives Genomic expression. 2) Gives Genomic location, gene aliases etc. as gene information. 3) Orthologous genes identified by MULTIZ alignments are given. 4) Isoform sequences are given. 5) Type of exons- Alternative or Constitute are given along with genomic position and number of EST and mRNA observed. 6) Intron type- Alternative or Constitutive, 5 site, 3 site, whether canonical or not and splice type, all information is provided. 7) Alternative Splicing information is provided. 1) Gives Genomic expression. 2) Gives Genomic location, gene aliases etc. as gene information. 3) Orthologous genes identified by MULTIZ alignments are given. 4) Isoform sequences are given. 5) Type of exons- Alternative or Constitute are given along with genomic position and number of EST and mRNA observed. 6) Intron type- Alternative or Constitutive, 5 site, 3 site, whether canonical or not and splice type, all information is provided. 7) Alternative Splicing information is provided. |
6 |
ASPic - Alternative Splicing Predictionhttp://t.caspur.it/ASPIC/index.php |
1) Detect the exon-intron structure of a gene. 2) Predicts constitutive and alternative splice sites. |
| Bonizzoni P, Rizzi R, Pesole G. ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences. BMC Bioinformatics. 2005 Oct 5;6:244. PubMed PMID:16207377; PubMed Central PMCID: PMC1276783. |
| 2005 | 100 |
1) Requires registration. 2) Gene name Brca1 and mybl2 as well as uploaded sequence didn't receive any results when used in the option of 'RUN Aspic'. 3) Provides option of retrieving Unigene ID for input. 4) Results are obtained in E-mail. 5) Gives genomic and transcript sequences. 6) Gene structure view is provided, showing Refseq exon, Novel exon, Refseq Intron, Novel intron, Fuzzy Intron, Canonical splice site and Non-Canonical splice site. 7) Shows 3'UTR and 5'UTR, Poly A site 8) Splice site details include the intron number, chromosome number, length, donor/ acceptor score, branching site score 9) Intron table provides information about relative and absolute start as well as relative and absolute end of intron, number of EST's, chromosome number, intron class, and Donor and acceptor site. 9) Gene information includes chromosome number, strand, position and length of gene. 1) Requires registration. 2) Gene name Brca1 and mybl2 as well as uploaded sequence didn't receive any results when used in the option of 'RUN Aspic'. 3) Provides option of retrieving Unigene ID for input. 4) Results are obtained in E-mail. 5) Gives genomic and transcript sequences. 6) Gene structure view is provided, showing Refseq exon, Novel exon, Refseq Intron, Novel intron, Fuzzy Intron, Canonical splice site and Non-Canonical splice site. 7) Shows 3'UTR and 5'UTR, Poly A site 8) Splice si |
7 |
ASPicDB - Alterenative Splicing Prediction databasehttp://t.caspur.it/ASPicDB/ |
| CastrignanF2 T, D'Antonio M, Anselmo A, Carrabino D, D'Onorio De Meo A,
D'Erchia AM, Licciulli F, Mangiulli M, Mignone F, Pavesi G, Picardi E, Riva A, Rizzi R, Bonizzoni P, Pesole G. ASPicDB: a database resource for alternative splicing analysis. Bioinformatics. 2008 May 15;24(10):1300-4. Epub 2008 Apr 3. PubMed PMID: 18388144. |
| 2008 | 100 |
|
8 |
Astalavista - Alternative splicing transcriptional landscape visualization toolhttp://genome.crg.es/astalavista/ |
Identifies complex Alternative Splice events by comparing all given transcripts. |
| Foissac S, Sammeth M. ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. Nucleic AcIDs Res. 2007 Jul;35(Web Server issue):W297-9. Epub 2007 May 7. PubMed PMID: 17485470; PubMed
Central PMCID: PMC1933205.
|
| 2007 | 100 |
1) The results can be browsed on UCSC browser. 2)Results can be downloaded in GTF or ASTA format. 3) Splice site details include the chromosome number, and the position of Alternative Splice sites. 4) Intron- Exon structure is also shown. 5) Types of Alternative Splice Events include exon skipping, alt acceptor and intron retention. 1) The results can be browsed on UCSC browser. 2)Results can be downloaded in GTF or ASTA format. 3) Splice site details include the chromosome number, and the position of Alternative Splice sites. 4) Intron- Exon structure is also shown. 5) Types of Alternative Splice Events include exon skipping, alt acceptor and intron retention. |
9 |
ChickGCE - Chicken Germ Cell ESThttp://chickGCE.snu.ac.kr |
1) Provides functional annotations, identification, and transcripts based on GEO.2) Provides comparison between two types of tissues and germ- cell- specific alternative splice events in the chicken. |
| Kim H, Lim D, Han BK, Sung S, Jeon M, Moon S, Kang Y, Nam J, Han JY. ChickGCE:
a novel germ cell EST database for studying the early developmental stage in
chickens. Genomics. 2006 Aug;88(2):252-7. Epub 2006 May 22. PubMed PMID:
16714094 |
| 2006 | 100 |
URL not working as on 14 Dec 2012 URL not working as on 14 Dec 2012 |
10 |
GeneSeqerhttp://deepc2.psi.iastate.edu/cgi-bin/gs.cgi |
Identify potential exon/intron structure in pre-mRNA by splice site prediction and spliced alignment. |
| Brendel V, Xing L, Zhu W. Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus. Bioinformatics. 2004 May 1;20(7):1157-69. Epub 2004 Feb 5. PubMed PMID: 14764557. |
| 2004 | 100 |
1) Looks for the EST matches. 2) E-mail notification. 3) Specialized GeneSeqer server at PlantGDB is used to align plant sequences. 1) Looks for the EST matches. 2) E-mail notification. 3) Specialized GeneSeqer server at PlantGDB is used to align plant sequences. |
11 |
GenomeThreaderhttp://www.plantgdb.org/cgi-bin/GenomeThreader/gth.cgi |
The GenomeThreader server allows you to perform spliced alignment of protein or EST/cDNA sequences to genomic DNA. |
| | Not available | 100 |
|
12 |
PolyA_DB 2http://polya.umdnj.edu/PolyA_DB2 |
It specializes in identification of Poly-A tail. |
| Lee JY, Yeh I, Park JY, Tian B. PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes. Nucleic AcIDs Res. 2007 Jan;35(Database issue):D165-8. PubMed PMID: 17202160; PubMed Central PMCID: PMC1899096. |
| 2007 | 100 |
URL not working as on 14 Dec 2012 URL not working as on 14 Dec 2012 |
13 |
Softberryhttp://linux1.softberry.com/berry.phtml |
1) Pattern based human gene structure prediction (multiple genes, both chains). 2) Find splice sites in genomic DNA using weight matrices. 3) BESTORF program analyses EST/mRNA sequences to predict potential coding fragments. 4) FGENE-SH is human gene prediction that allows to predict genes containing minor variants of donor splice sites (GC sites). 5) Looks for Pattern-based human multiple variants (alternative splicing) of potential genes in genomic DNA. 6) Finding potential 5'-, internal and 3'-coding exons. 7) Rna SPL is used for For exon-exon junctions positions in human cDNA. |
| | Not available | 100 |
|
14 |
SplicePredictorhttp://deepc2.psi.iastate.edu/cgi-bin/sp.cgi |
Identifies potential splice sites in (plant) pre-mRNA. |
| | Not available | 100 |
1) Gives information about acceptor and donor site. 2) Gives information about site location and sequence. 3) Also gives information about the site quality. 4) Results can be obtained by e-mail. 1) Gives information about acceptor and donor site. 2) Gives information about site location and sequence. 3) Also gives information about the site quality. 4) Results can be obtained by e-mail. |