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orthology_databases [2023/11/14 15:50] Paul Thomas |
orthology_databases [2023/11/15 15:50] Marina Marcet Houben |
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| | [[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 | 2023 | yearly | yes | all domains of life | [[http://pantherdb.org/panther/summaryStats.jsp|143]] | [[http://pantherdb.org/services/index.jsp|yes]] | yes | | | [[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 | 2016 | | yes | all domains of life | >1000 | 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 | | ||