PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-2 (2)
 

Clipboard (0)
None
Journals
Authors
Year of Publication
Document Types
1.  Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees 
Briefings in Bioinformatics  2011;12(5):423-435.
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.
doi:10.1093/bib/bbr034
PMCID: PMC3178055  PMID: 21737420
conceptual comparison; phylogenomic databases; quality assessment; reference gene trees
2.  When orthologs diverge between human and mouse 
Briefings in Bioinformatics  2011;12(5):436-441.
Despite the common assumption that orthologs usually share the same function, there have been various reports of divergence between orthologs, even among species as close as mammals. The comparison of mouse and human is of special interest, because mouse is often used as a model organism to understand human biology. We review the literature on evidence for divergence between human and mouse orthologous genes, and discuss it in the context of biomedical research.
doi:10.1093/bib/bbr031
PMCID: PMC3178054  PMID: 21677033
orthology; expression divergence; alternative splicing; copy number variants; phenotypic divergence

Results 1-2 (2)