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| orthology_databases [2017/06/08 17:44] – Adrian Altenhoff | orthology_databases [2023/11/24 11:57] (current) – Updated Metaphors Diego Fuentes |
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| //If you know of any other database, please edit this page directly or contact us. The detailed table is the new preferred format--please help us complete it// | //If you know of any other database, please edit this page directly or contact us. The detailed table is the new preferred format--please help us complete it// |
| ^ Database ^ Description / Scientific focus applications (Max. 2 sentences) ^ Last updated ^ Update frequency ^ QFO Reference Proteomes ^ Taxonomic range covered ^ Number of organisms ^ Web service available ^ OrthoXML available ^ | ^ Database ^ Description / Scientific focus applications (Max. 2 sentences) ^ Last updated ^ Update frequency ^ QFO Reference Proteomes ^ Taxonomic range covered ^ Number of organisms ^ Web service available ^ OrthoXML available ^ |
| | [[http://orthodb.org/|OrthoDB]] | Comparative genomics, gene function inference, phylogenomics | [[http://www.ncbi.nlm.nih.gov/pubmed?cmd=Search&term=27899580|2016]] | yearly | no | all domains of life and viruses | >4000 Prok., 588 Euk., & >3000 vir. | [[http://www.orthodb.org/?page=api|yes]] | no | | |
| | [[http://betaorthology.phylomedb.org/|metaPhOrs]] | Phylogeny-based orthologs and paralogs computed using a consistency-based algorithms and phylogenetic trees available in 12 public repositories | 2015 | | yes | all domains of life | 2,714 | yes | no | | |
| | [[http://phylomedb.org/|PhylomeDB]] | Genome-wide collection of gene evolutionary histories, and phylogeny-based orthology and paralogy prediction | 2016 | | yes | all domains of life | >1000 | yes | yes | | |
| | [[http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/|DIOPT]] | Integrative ortholog prediction tool of 10 algorithms | 2016 | | partially | major model organisms | 9 | yes | no | | | [[http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/|DIOPT]] | Integrative ortholog prediction tool of 10 algorithms | 2016 | | partially | major model organisms | 9 | yes | no | |
| | [[http://www.ensembl.org/|Ensembl Compara]] | [[http://www.ensembl.org/info/genome/compara/|Evolutionary relationships among Ensembl species genes]]; Projection of gene names and GO annotations | 2016 | 4-5x / year | no | all domains of life through 6 //divisions// (sets of species) | [[http://www.ensembl.org/info/about/species.html|66 chordates]] and [[http://ensemblgenomes.org/info/genomes|240 others]] | [[http://rest.ensembl.org/|yes]] | yes | | |
| | [[http://eggnogdb.embl.de/|eggNOG]] | A database for phylogenetically refined Orthologous Groups and functional annotation. | 2016 | biennial | no | all domains of life (plus viruses) | 1793 prokaryote proteomes, 238 eukaryotes, 352 viruses | [[http://eggnogdb.embl.de/#/app/api|yes]] | no | | | [[http://eggnogdb.embl.de/|eggNOG]] | A database for phylogenetically refined Orthologous Groups and functional annotation. | 2016 | biennial | no | all domains of life (plus viruses) | 1793 prokaryote proteomes, 238 eukaryotes, 352 viruses | [[http://eggnogdb.embl.de/#/app/api|yes]] | no | |
| | [[http://inparanoid.sbc.su.se/|InParanoid]] | Database of 2-species ortholog groups with inparalogs; inparalogs and seed orthologs are assigned a confidence score | 2014 | | yes | all domains of life, mostly eukaryotic | [[http://inparanoid.sbc.su.se/cgi-bin/summary.cgi|273]] | no | yes | | | [[http://www.ensembl.org/|Ensembl Compara]] | [[http://www.ensembl.org/info/genome/compara/|Evolutionary relationships among Ensembl species genes]]; Projection of gene names and GO annotations | 2016 | 4-5x / year | no | all domains of life through 6 //divisions// (sets of species) | [[http://www.ensembl.org/info/about/species.html|66 chordates]] and [[http://ensemblgenomes.org/info/genomes|240 others]] | [[http://rest.ensembl.org/|yes]] | yes | |
| | | [[http://fungipath.i2bc.paris-saclay.fr/|FUNGIpath]] | FUNGIpath is a web service dedicated to the exploration of fungal metabolism. More info on the database [[http://fungipath.i2bc.paris-saclay.fr/help.php|here]]. More info on the orthologs detection method [[http://bim.igmors.u-psud.fr/mario/|here]]. | 2014 | variable | yes [[http://bim.igmors.u-psud.fr/mario/]] | Fungi | 165 | yes | yes for the QFO reference proteomes | |
| | | [[http://www.greenphyl.org/|GreenPhylDB]] | Database for comparative and functional genomics in plants. gene family clustering, manual curation and phylogenomic inference of orthologs | 2014 | variable | no | Viridiplantae | 37 | yes | no | |
| | [[http://hieranoidb.sbc.su.se/|HieranoiDB]] | Database of ortholog trees inferred by Hieranoid; speciation and duplication nodes are marked; inparalogs are assigned a confidence score | 2016 | | yes | all domains of life | 66 | no | yes | | | [[http://hieranoidb.sbc.su.se/|HieranoiDB]] | Database of ortholog trees inferred by Hieranoid; speciation and duplication nodes are marked; inparalogs are assigned a confidence score | 2016 | | yes | all domains of life | 66 | no | yes | |
| | [[http://omabrowser.org/|OMA]] | [[http://omabrowser.org/oma/about|Phylogenetic reconstruction, function prediction and ancestral | | [[http://inparanoidb.sbc.su.se/|InParanoiDB]] | Database of 2-species full-length protein and domain ortholog groups with inparalogs; inparalogs and seed orthologs are assigned a confidence score | 2023 | | yes | all domains of life | [[https://inparanoidb9.sbc.su.se/statistics/|640]] | no | yes | |
| genome content through different types of orthologous groups]] | 2017 | 2x / year | partially | all domains of life | >2000 | [[http://omabrowser.org/oma/APISOAP|yes]] | yes | | | [[http://orthology.phylomedb.org/|metaPhOrs]] | Phylogeny-based orthologs and paralogs computed using a consistency-based algorithms and phylogenetic trees available in 12 public repositories | 2021 | | yes | all domains of life | 6,384 | yes | no | |
| | | [[http://omabrowser.org/|OMA]] | [[http://omabrowser.org/oma/about|Phylogenetic reconstruction, function prediction and ancestral genome content through different types of orthologous groups]] | [[https://omabrowser.org/static/image/history.png|2023]] | 2x / year | partially | all domains of life | >2500 | [[http://omabrowser.org/api/docs|yes]] | yes | |
| | | [[http://orthodb.org/|OrthoDB]] | Comparative genomics, gene function inference, phylogenomics | [[http://www.ncbi.nlm.nih.gov/pubmed?cmd=Search&term=27899580|2016]] | yearly | no | all domains of life and viruses | >4000 Prok., 588 Euk., & >3000 vir. | [[http://www.orthodb.org/?page=api|yes]] | no | |
| | | [[http://www.lbgi.fr/orthoinspector/|OrthoInspector]] | Databases of pairwise orthology and inparalogy relationships | 2015 | | yes | all domains of life | 259 Eukaryotes, 1688 Prokaryotes | yes |yes | |
| | [[http://www.pathogenomics.sfu.ca/ortholugedb/|OrtholugeDB]] | Ortholog predictions for completely sequenced bacterial and archaeal genomes, with additional assessment using Ortholuge to improve specificity | 2016 | 1x / year | no | bacteria and archaea | >2000 | yes | yes | | | [[http://www.pathogenomics.sfu.ca/ortholugedb/|OrtholugeDB]] | Ortholog predictions for completely sequenced bacterial and archaeal genomes, with additional assessment using Ortholuge to improve specificity | 2016 | 1x / year | no | bacteria and archaea | >2000 | yes | yes | |
| | [[http://www.pantherdb.org/|PANTHER]] | Evolutionary relationships among model organism genes; Inference of gene function using GO terms | 2016 | yearly | yes | all domains of life | [[http://pantherdb.org/panther/summaryStats.jsp|104]] | [[http://pantherdb.org/help/PANTHERhelp.jsp#V.A.|yes]] | no | | | [[http://www.pantherdb.org/|PANTHER]] | Evolutionary relationships among model organism genes; Inference of gene function using GO terms | 2023 | yearly | yes | all domains of life | [[http://pantherdb.org/panther/summaryStats.jsp|143]] | [[http://pantherdb.org/services/index.jsp|yes]] | yes | |
| | | [[http://phylomedb.org/|PhylomeDB]] | Genome-wide collection of gene evolutionary histories, and phylogeny-based orthology and paralogy prediction | 2023 | | yes | all domains of life | >1000 | yes | yes | |
| | [[http://bioinformatics.psb.ugent.be/plaza/|PLAZA]] | Plant comparative genomics database, focusing on dicots, monocots and green algae. More info about data types [[http://bioinformatics.psb.ugent.be/knowledge/wiki-plaza/data_content|here]]| 2014 | | no | Viridiplantae | Dicots 3.0 [[http://bioinformatics.psb.ugent.be/plaza/versions/plaza_v3_dicots/|31]], Monocots 3.0 [[http://bioinformatics.psb.ugent.be/plaza/versions/plaza_v3_monocots/|16]] | no | no | | | [[http://bioinformatics.psb.ugent.be/plaza/|PLAZA]] | Plant comparative genomics database, focusing on dicots, monocots and green algae. More info about data types [[http://bioinformatics.psb.ugent.be/knowledge/wiki-plaza/data_content|here]]| 2014 | | no | Viridiplantae | Dicots 3.0 [[http://bioinformatics.psb.ugent.be/plaza/versions/plaza_v3_dicots/|31]], Monocots 3.0 [[http://bioinformatics.psb.ugent.be/plaza/versions/plaza_v3_monocots/|16]] | no | no | |
| | [[http://www.treefam.org/|TreeFam]] | [[http://www.treefam.org/browse|Catalogue of gene families]]; [[http://www.treefam.org/help#tabview=tab1|Phylogenetic reconstruction]] | 2012 | Next update in 2015 | no | metazoans + model eukaryotes | [[http://www.treefam.org/browse#tabview=tab1|109]] | no | no | | | [[http://www.treefam.org/|TreeFam]] | [[http://www.treefam.org/browse|Catalogue of gene families]]; [[http://www.treefam.org/help#tabview=tab1|Phylogenetic reconstruction]] | 2012 | Next update in 2015 | no | metazoans + model eukaryotes | [[http://www.treefam.org/browse#tabview=tab1|109]] | no | no | |
| | [[http://www.greenphyl.org/|GreenPhylDB]] | Database for comparative and functional genomics in plants. gene family clustering, manual curation and phylogenomic inference of orthologs | 2014 | variable | no | Viridiplantae | 37 | yes | no | | |
| | [[http://wormhole.jax.org/|WORMHOLE]] | Machine learning-based integration of 17 ortholog prediction methods. | 2016 | variable | no | major model organisms | 6 | yes | no | | | [[http://wormhole.jax.org/|WORMHOLE]] | Machine learning-based integration of 17 ortholog prediction methods. | 2016 | variable | no | major model organisms | 6 | yes | no | |
| | [[http://fungipath.i2bc.paris-saclay.fr/|FUNGIpath]] | FUNGIpath is a web service dedicated to the exploration of fungal metabolism. More info on the database [[http://fungipath.i2bc.paris-saclay.fr/help.php|here]]. More info on the orthologs detection method [[http://bim.igmors.u-psud.fr/mario/|here]]. | 2014 | variable | yes [[http://bim.igmors.u-psud.fr/mario/]] | Fungi | 165 | yes | yes for the QFO reference proteomes | | |
| == Other databases: == | == Other databases: == |
| - [[http://www.ncbi.nlm.nih.gov/COG|COGs/TWOGa/KOGs]] | - [[http://www.ncbi.nlm.nih.gov/COG|COGs/TWOGa/KOGs]] |
| - HOPS | - HOPS |
| - INVHOGEN | - INVHOGEN |
| - [[http://hieranoid.sbc.su.se|Hieranoid]] | |
| - [[http://inparanoid.sbc.su.se|InParanoid]] | |
| - [[http://www.genome.jp/kegg/ko.html|KEGG Orthology]] | - [[http://www.genome.jp/kegg/ko.html|KEGG Orthology]] |
| - [[http://orthology.phylomedb.org/|MetaPhOrs]] | - [[http://orthology.phylomedb.org/|MetaPhOrs]] |
| - [[http://cegg.unige.ch/orthodb|OrthoDB]] ([[http://en.wikipedia.org/wiki/OrthoDB|OrthoDB on Wikipedia]]) | - [[http://cegg.unige.ch/orthodb|OrthoDB]] ([[http://en.wikipedia.org/wiki/OrthoDB|OrthoDB on Wikipedia]]) |
| - [[http://nypg.bio.nyu.edu/orthologid/|OrthologID]] | - [[http://nypg.bio.nyu.edu/orthologid/|OrthologID]] |
| - [[http://lbgi.igbmc.fr/orthoinspector/|OrthoInspector]] | |
| - [[http://www.orthomcl.org/|OrthoMCL]] | - [[http://www.orthomcl.org/|OrthoMCL]] |
| - PhIGs | - PhIGs |
| - PHOG | - PHOG |
| - [[http://phylomedb.org/|PhylomeDB]] | - [[http://phylomedb.org/|PhylomeDB]] |
| - [[http://bioinformatics.psb.ugent.be/plaza/|PLAZA]] | |
| - [[http://ppod.princeton.edu|P-POD]] | - [[http://ppod.princeton.edu|P-POD]] |
| - [[http://www.bioinformatics.nl/progmap|ProGMap]] | - [[http://www.bioinformatics.nl/progmap|ProGMap]] |
