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

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 probabilistic alignments produced by the probA program with structural alignments produced by four different structure alignment algorithms. There is significant overlap between the solution spaces of structural alig...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Michael L. Sierk, Michael E. Smoot, Ellen J. Bass, William R. Pearson
• Keywords: BMCBI 2010, Sequence Alignment, Structural Alignments, Suboptimal Sequence Alignments