Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments.

ABSTRACT:

Background

While the pairwise alignments produced by sequence similarity searches are a powerful tool for identifying homologous proteins - proteins that share a common ancestor and a similar structure; pairwise sequence alignments often fail to represent accurately the structural alignments inferred from three-dimensional coordinates. Since sequence alignment algorithms produce optimal alignments, the best structural alignments must reflect suboptimal sequence alignment scores. Thus, we have examined a range of suboptimal sequence alignments and a range of scoring parameters to understand better which sequence alignments are likely to be more structurally accurate.

Results

We compared near-optimal protein sequence alignments produced by the Zuker algorithm and a set of prob

SUBMITTER: Sierk ML 

PROVIDER: S-EPMC2850363 | biostudies-literature | 2010 Mar

REPOSITORIES: biostudies-literature