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 independent and powerful measure of evolutionary relationships that does not rely on potentially subjective sequence alignment. We demonstrate that evolutionary relationships can be measured with phylogenetic profiles, and therefore propose that these measurements can provide key insights into relationships among distantly related and/or rapidly evolving proteins.

authors

Chang GS,Hong Y,Ko KD,Bhardwaj G,Holmes EC,Patterson RL,van Rossum DB

doi

10.1073/pnas.0803860105

subject

Has Abstract

pub_date

2008-09-09 00:00:00

pages

13474-9

issue

36

eissn

0027-8424

issn

1091-6490

pii

0803860105

journal_volume

105

pub_type

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