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orthology_databases [2017/06/06 22:54] Erik Sonnhammer |
orthology_databases [2017/07/07 14:32] Erik Sonnhammer |
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| | [[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://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.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 | | ||
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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 49: | Line 47: | ||
| - 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]] | ||