A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation.

ABSTRACT: Accurate orthology prediction is crucial for many applications in the post-genomic era. The lack of broadly accepted benchmark tests precludes a comprehensive analysis of orthology inference. So far, functional annotation between orthologs serves as a performance proxy. However, this violates the fundamental principle of orthology as an evolutionary definition, while it is often not applicable due to limited experimental evidence for most species. Therefore, we constructed high quality "gold standard" orthologous groups that can serve as a benchmark set for orthology inference in bacterial species. Herein, we used this dataset to demonstrate 1) why a manually curated, phylogeny-based dataset is more appropriate for benchmarking orthology than other popular practices and 2) how it guides da

SUBMITTER: Trachana K 

PROVIDER: S-EPMC4219706 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature