,
Phylogenetic and Functional Assessment of Orthologs Inference
PLoS Comput Biol, 5 (1): e1000262 (января 2009)
DOI: 10.1371/journal.pcbi.1000262
Аннотация
<title>Author Summary</title>
<p>The identification of orthologs, pairs of homologous genes in different species
that started diverging through speciation events, is a central problem in
genomics with applications in many research areas, including comparative
genomics, phylogenetics, protein function annotation, and genome rearrangement.
An increasing number of projects aim at inferring orthologs from complete
genomes, but little is known about their relative accuracy or coverage. Because
the exact evolutionary history of entire genomes remains largely unknown,
predictions can only be validated indirectly, that is, in the context of the
different applications of orthology. The few comparison studies published so far
have asssessed orthology exclusively from the expectation that orthologs have
conserved protein function. In the present work, we introduce methodology to
verify orthology in terms of phylogeny and perform a comprehensive comparison of
nine leading ortholog inference projects and two methods using both phylogenetic
and functional tests. The results show large variations among the different
projects in terms of performances, which indicates that the choice of orthology
database can have a strong impact on any downstream analysis.</p>
