Protein sequence-similarity search acceleration using a heuristic algorithm with a sensitive matrix.

ABSTRACT: Protein database search for public databases is a fundamental step in the target selection of proteins in structural and functional genomics and also for inferring protein structure, function, and evolution. Most database search methods employ amino acid substitution matrices to score amino acid pairs. The choice of substitution matrix strongly affects homology detection performance. We earlier proposed a substitution matrix named MIQS that was optimized for distant protein homology search. Herein we further evaluate MIQS in combination with LAST, a heuristic and fast database search tool with a tunable sensitivity parameter m, where larger m denotes higher sensitivity. Results show that MIQS substantially improves the homology detection and alignment quality performance of LAST across div

SUBMITTER: Lim K 

PROVIDER: S-EPMC5274646 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature