Phylogenetic profiles reveal evolutionary relationships within the "twilight zone" of sequence similarity.

ABSTRACT: Inferring evolutionary relationships among highly divergent protein sequences is a daunting task. In particular, when pairwise sequence alignments between protein sequences fall <25% identity, the phylogenetic relationships among sequences cannot be estimated with statistical certainty. Here, we show that phylogenetic profiles generated with the Gestalt Domain Detection Algorithm-Basic Local Alignment Tool (GDDA-BLAST) are capable of deriving, ab initio, phylogenetic relationships for highly divergent proteins in a quantifiable and robust manner. Notably, the results from our computational case study of the highly divergent family of retroelements accord with previous estimates of their evolutionary relationships. Taken together, these data demonstrate that GDDA-BLAST provides an independe

SUBMITTER: Chang GS 

PROVIDER: S-EPMC2527991 | biostudies-literature | 2008 Sep

REPOSITORIES: biostudies-literature