Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions.

ABSTRACT: Detection of protein homology via sequence similarity has important applications in biology, from protein structure and function prediction to reconstruction of phylogenies. Although current methods for aligning protein sequences are powerful, challenges remain, including problems with homologous overextension of alignments and with regions under convergent evolution. Here, we test the ability of the profile hidden Markov model method HMMER3 to correctly assign homologous sequences to >13,000 manually curated families from the Pfam database. We identify problem families using protein regions that match two or more Pfam families not currently annotated as related in Pfam. We find that HMMER3 E-value estimates seem to be less accurate for families that feature periodic patterns of compositio

SUBMITTER: Mistry J 

PROVIDER: S-EPMC3695513 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature