Improving the alignment quality of consistency based aligners with an evaluation function using synonymous protein words.

ABSTRACT: Most sequence alignment tools can successfully align protein sequences with higher levels of sequence identity. The accuracy of corresponding structure alignment, however, decreases rapidly when considering distantly related sequences (<20% identity). In this range of identity, alignments optimized so as to maximize sequence similarity are often inaccurate from a structural point of view. Over the last two decades, most multiple protein aligners have been optimized for their capacity to reproduce structure-based alignments while using sequence information. Methods currently available differ essentially in the similarity measurement between aligned residues using substitution matrices, Fourier transform, sophisticated profile-profile functions, or consistency-based approaches, more recently

SUBMITTER: Lin HN 

PROVIDER: S-EPMC3229492 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature