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--- orthology_databases [2016/08/19 09:32]
Admin
+++ orthology_databases [2023/11/15 15:51]
Marina Marcet Houben
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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 ^
 | [[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://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://betaorthology.phylomedb.org/|metaPhOrs]] | Phylogeny-based orthologs and paralogs computed using a consistency-based algorithms and phylogenetic trees available in 12 public repositories | 2020 | | 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]] | [[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.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://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: ==
   - [[http://www.ncbi.nlm.nih.gov/COG|COGs/TWOGa/KOGs]]
@@ Line 19: / Line 27: @@
   - [[http://eggnog.embl.de/|eggNOG]]
   - [[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://greenphyl.cirad.fr/|GreenPhylDB]]
   - [[http://www.genenames.org/cgi-bin/hcop.pl/|HCOP (meta-database)]]
   - [[http://www.ncbi.nlm.nih.gov/homologene|HomoloGene]]
@@ Line 29: / Line 35: @@
   - HOPS
   - INVHOGEN
-  - [[http://hieranoid.sbc.su.se|Hieranoid]]
-  - [[http://inparanoid.sbc.su.se|InParanoid]]
   - [[http://www.genome.jp/kegg/ko.html|KEGG Orthology]]
   - [[http://orthology.phylomedb.org/|MetaPhOrs]]
@@ Line 38: / Line 42: @@
   - [[http://cegg.unige.ch/orthodb|OrthoDB]] ([[http://en.wikipedia.org/wiki/OrthoDB|OrthoDB on Wikipedia]])
   - [[http://nypg.bio.nyu.edu/orthologid/|OrthologID]]
-  - [[http://lbgi.igbmc.fr/orthoinspector/|OrthoInspector]]
   - [[http://www.orthomcl.org/|OrthoMCL]]
   - PhIGs
   - PHOG
   - [[http://phylomedb.org/|PhylomeDB]]
-  - [[http://bioinformatics.psb.ugent.be/plaza/|PLAZA]]
   - [[http://ppod.princeton.edu|P-POD]]
   - [[http://www.bioinformatics.nl/progmap|ProGMap]]