Evaluating ortholog prediction algorithms in a yeast model clade.

ABSTRACT:

Background

Accurate identification of orthologs is crucial for evolutionary studies and for functional annotation. Several algorithms have been developed for ortholog delineation, but so far, manually curated genome-scale biological databases of orthologous genes for algorithm evaluation have been lacking. We evaluated four popular ortholog prediction algorithms (MultiParanoid; and OrthoMCL; RBH: Reciprocal Best Hit; RSD: Reciprocal Smallest Distance; the last two extended into clustering algorithms cRBH and cRSD, respectively, so that they can predict orthologs across multiple taxa) against a set of 2,723 groups of high-quality curated orthologs from 6 Saccharomycete yeasts in the Yeast Gene Order Browser.

Results

Examination of sensitivity [TP/(TP+FN)], specificity [TN/(TN

SUBMITTER: Salichos L 

PROVIDER: S-EPMC3076445 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature