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orthology_databases [2017/03/06 17:46] Evgeny Zdobnov added OrthoDB |
orthology_databases [2017/08/10 14:12] odilelecompte |
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| | [[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://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://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://omabrowser.org/|OMA]] | [[http://omabrowser.org/oma/about|Phylogenetic reconstruction, function prediction and ancestral | ||
| - | genome content through different types of orthologous groups]] | 2016 | 2x / year | partially | all domains of life | >2000 | [[http://omabrowser.org/oma/APISOAP|yes]] | 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://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.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.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 | 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://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 | | ||
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| - 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]] | ||
| Line 43: | Line 43: | ||
| - [[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]] | ||