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orthology_databases [2016/08/19 09:32]
Admin
orthology_databases [2023/11/24 12:57] (current)
Diego Fuentes Updated Metaphors
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 ^ 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://​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://​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://​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://​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://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://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://​omabrowser.org/​|OMA]] | [[http://​omabrowser.org/​oma/​about|Phylogenetic reconstruction,​ function prediction and ancestral ​ +| [[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 | 
-genome content through different types of orthologous groups]] | 2016 | 2x / year  | partially | all domains of life | >2000 | [[http://​omabrowser.org/​oma/APISOAP|yes]] ​ | 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://​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 
 +| [[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://​wormhole.jax.org/​|WORMHOLE]] | Machine learning-based integration of 17 ortholog prediction methods. | 2016 | variable | no |  major model organisms | 6  | yes | no |
 == 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://​eggnog.embl.de/​|eggNOG]]   - [[http://​eggnog.embl.de/​|eggNOG]]
   - [[http://​compbio.dfci.harvard.edu/​tgi/​ego/​|EGO]]   - [[http://​compbio.dfci.harvard.edu/​tgi/​ego/​|EGO]]
-  - [[http://​www.fungipath.u-psud.fr|FUNGIpath]] 
   - [[http://​goods.ibms.sinica.edu.tw/​goods/​|Gene-Oriented Ortholog Database]]   - [[http://​goods.ibms.sinica.edu.tw/​goods/​|Gene-Oriented Ortholog Database]]
-  - [[http://​greenphyl.cirad.fr/​|GreenPhylDB]] 
   - [[http://​www.genenames.org/​cgi-bin/​hcop.pl/​|HCOP (meta-database)]]   - [[http://​www.genenames.org/​cgi-bin/​hcop.pl/​|HCOP (meta-database)]]
   - [[http://​www.ncbi.nlm.nih.gov/​homologene|HomoloGene]]   - [[http://​www.ncbi.nlm.nih.gov/​homologene|HomoloGene]]
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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]]
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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
   - 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]]