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Created on: 09-Sep-2012
Last updated on: 09-Sep-2012
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Total resources - 36
A list of resources for orthologs
Sravanthi Davuluri and Akhilesh Bajpai (Correspondence: Acharya KK, kshitish@ibab.ac.in)
S.No
Resources
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Short description*
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More Details
Method Description
Click to Edit / Add comments
1
GOOD - Gene-Oriented Ortholog Database
http://goods.ibms.sinica.edu.tw/goods
For comparing paired orthologous genomic loci in the transcriptional and functional aspects
1
2
PANTHER - Protein ANalysis THrough Evolutionary Relationships
http://www.pantherdb.org
Classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships
50
3
COGs - Clusters of Orthologous Groups of proteins
http://www.ncbi.nlm.nih.gov/COG
Phylogenetic classification of proteins encoded in complete genomes
74
4
HomoloGene
http://www.ncbi.nlm.nih.gov/homologene
Automated detection of homologs among the annotated genes
76
5
Plaza
http://bioinformatics.psb.ugent.be/plaza
Evolutionary analyses and data mining within the green plant lineage
89
6
InParanoid - Eukaryotic Ortholog Groups
http://inparanoid.sbc.su.se
94
7
POGs - Putative Orthologous Groups
http://cas-pogs.uoregon.edu/#/
97
8
eggNOG - evolutionary genealogy of genes: Non-supervised Orthologous Groups
http://eggnog.embl.de
Orthologous groups of genes
98
9
KEGG ORTHOLOGY (KO) Database
http://www.genome.jp/kegg/ko.html
Linking genomes to pathways by ortholog annotation
98
10
PhylomeDB
http://phylomedb.org
Complete collections of gene phylogenies
98
11
OrthoDB - The Hierarchical Catalog of Eukaryotic Orthologs
http://cegg.unige.ch/orthodb5
Catalog of eukaryotic orthologous protein-coding genes
99
12
ATGCs - Alignable Tight Genomic Clusters
http://atgc.lbl.gov/atgc
Closely Related Prokaryotic Genomes
100
13
BLASTO - BLAST on Orthologous groups
http://oxytricha.princeton.edu/BlastO
100
14
DOOP - Database of Orthologous Promoters
http://doop.abc.hu
Eukaryotic promoter sequences that facilitates the recognition of regulatory sites conserved between species
100
15
EGO - Eukaryotic Gene Orthologues
http://compbio.dfci.harvard.edu/tgi/ego
100
16
Ensembl Compara
http://www.ensembl.org/info/docs/compara
100
17
Evola
http://www.h-invitational.jp/evola/search.html
Ortholog information between human and fourteen vertebrates
100
18
GreenPhyl
http://www.greenphyl.org/cgi-bin/index.cgi
A catalog of gene families and comparative and functional genomics in plants
100
19
HCOP - HGNC Comparison of Orthology Predictions
http://www.genenames.org/cgi-bin/hcop.pl
100
20
HOBACGEN - Homologous Bacterial Genes Database
http://pbil.univ-lyon1.fr/databases/hobacgen.html
100
21
HOGENOM - Database of Complete Genome Homologous Genes Families
http://pbil.univ-lyon1.fr/databases/hogenom
100
22
Isobase - IsoRank PPI Network Alignment Based Ortholog Database
http://groups.csail.mit.edu/cb/mna/isobase
Functionally related orthologs
100
23
KEGG SSDB Database
http://www.kegg.jp/kegg/ssdb
Orthologs/paralogs, conserved gene clusters, and sequence motifs
100
24
MetaPhOrs
http://orthology.phylomedb.org
Rpository of phylogeny-based orthology and paralogy predictions
100
25
OrthoDisease - A Database of Human Disease Orthologs
http://orthodisease.sbc.su.se
100
26
OrthoInspector
http://lbgi.igbmc.fr/orthoinspector
Orthology/paralogy analysis
100
27
OrthologID
http://nypg.bio.nyu.edu/orthologid
Automates gene orthology determination within a character-based phylogenetic framework
100
28
OrthoMaM - Orthologous Mammalian Markers
http://www.orthomam.univ-montp2.fr
A database of orthologous genomic markers for placental mammal phylogenetics
100
29
OrthoMCL DB
http://www.orthomcl.org/cgi-bin/OrthoMclWeb.cgi
Ortholog Groups of Protein Sequences from Multiple Genomes
100
30
P-POD - Princeton Protein Orthology Database
http://ppod.princeton.edu
100
31
Primate Orthologous Exon Database
http://giladlab.uchicago.edu/orthoExon
A catalog of unique, non-overlapping, orthologous exon regions in the genomes of human, chimpanzee, and rhesus macaque
100
32
ProGmap
http://www.bioinformatics.nl/progmap
100
33
Proteinortho - Orthology detection tool
http://www.bioinf.uni-leipzig.de/Software/proteinortho
100
34
Roundup
http://roundup.hms.harvard.edu
Orthologs and their evolutionary distances
100
35
TreeFam - Tree families database
http://www.treefam.org
Curated resource that gives reliable information about ortholog and paralog assignments
100
36
YOGY
http://www.bahlerlab.info/YOGY
Orthologous proteins
100
Please use the following to cite:
"Sravanthi Davuluri and Akhilesh Bajpai (Correspondence: Acharya KK, kshitish@ibab.ac.in), A list of resources for orthologs; In: Startbioinfo; 09 Sep 2012, /cgi-bin/prelimresources.pl?tn=orthologs"
Disclaimer
copyright © Dr. Kshitish Acharya K; all rights reserved
Some of the sentences in this column may be quoted from the original website of the corresponding tool or database
