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.
journal_name
Proc Natl Acad Sci U S Aauthors
Chang GS,Hong Y,Ko KD,Bhardwaj G,Holmes EC,Patterson RL,van Rossum DBdoi
10.1073/pnas.0803860105subject
Has Abstractpub_date
2008-09-09 00:00:00pages
13474-9issue
36eissn
0027-8424issn
1091-6490pii
0803860105journal_volume
105pub_type
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