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BMCBI
2010

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

9 years 2 months ago
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...
Michael L. Sierk, Michael E. Smoot, Ellen J. Bass,
Added 08 Dec 2010
Updated 08 Dec 2010
Type Journal
Year 2010
Where BMCBI
Authors Michael L. Sierk, Michael E. Smoot, Ellen J. Bass, William R. Pearson
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