Fold homology detection using sequence fragment composition profiles of proteins.

ABSTRACT: The effectiveness of sequence alignment in detecting structural homology among protein sequences decreases markedly when pairwise sequence identity is low (the so-called "twilight zone" problem of sequence alignment). Alternative sequence comparison strategies able to detect structural kinship among highly divergent sequences are necessary to address this need. Among them are alignment-free methods, which use global sequence properties (such as amino acid composition) to identify structural homology in a rapid and straightforward way. We explore the viability of using tetramer sequence fragment composition profiles in finding structural relationships that lie undetected by traditional alignment. We establish a strategy to recast any given protein sequence into a tetramer sequence fragment

SUBMITTER: Solis AD 

PROVIDER: S-EPMC2933786 | biostudies-literature | 2010 Oct

REPOSITORIES: biostudies-literature