Abstract:
:Phylogenomic databases provide orthology predictions for species with fully sequenced genomes. Although the goal seems well-defined, the content of these databases differs greatly. Seven ortholog databases (Ensembl Compara, eggNOG, HOGENOM, InParanoid, OMA, OrthoDB, Panther) were compared on the basis of reference trees. For three well-conserved protein families, we observed a generally high specificity of orthology assignments for these databases. We show that differences in the completeness of predicted gene relationships and in the phylogenetic information are, for the great majority, not due to the methods used, but to differences in the underlying database concepts. According to our metrics, none of the databases provides a fully correct and comprehensive protein classification. Our results provide a framework for meaningful and systematic comparisons of phylogenomic databases. In the future, a sustainable set of 'Gold standard' phylogenetic trees could provide a robust method for phylogenomic databases to assess their current quality status, measure changes following new database releases and diagnose improvements subsequent to an upgrade of the analysis procedure.
journal_name
Brief Bioinformjournal_title
Briefings in bioinformaticsauthors
Boeckmann B,Robinson-Rechavi M,Xenarios I,Dessimoz Cdoi
10.1093/bib/bbr034subject
Has Abstractpub_date
2011-09-01 00:00:00pages
423-35issue
5eissn
1467-5463issn
1477-4054pii
bbr034journal_volume
12pub_type
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journal_title:Briefings in bioinformatics
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journal_title:Briefings in bioinformatics
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journal_title:Briefings in bioinformatics
pub_type: 历史文章,杂志文章,评审
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journal_title:Briefings in bioinformatics
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