Adjusting scoring matrices to correct overextended alignments.

ABSTRACT:

Motivation

Sequence similarity searches performed with BLAST, SSEARCH and FASTA achieve high sensitivity by using scoring matrices (e.g. BLOSUM62) that target low identity (<33%) alignments. Although such scoring matrices can effectively identify distant homologs, they can also produce local alignments that extend beyond the homologous regions.

Results

We measured local alignment start/stop boundary accuracy using a set of queries where the correct alignment boundaries were known, and found that 7% of BLASTP and 8% of SSEARCH alignment boundaries were overextended. Overextended alignments include non-homologous sequences; they occur most frequently between sequences that are more closely related (>33% identity). Adjusting the scoring matrix to reflect the identity of the hom

SUBMITTER: Mills LJ 

PROVIDER: S-EPMC3834790 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature