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orthology_databases [2017/07/07 14:32]
Erik Sonnhammer
orthology_databases [2017/11/30 15:44]
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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 inparalogsinparalogs ​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://​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 | 
-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://​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://​omabrowser.org/​|OMA]] | [[http://​omabrowser.org/​oma/​about|Phylogenetic reconstruction,​ function prediction and ancestral 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://​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    | 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://​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://​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]]
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   - [[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