BALSA: Bayesian algorithm for local sequence alignment
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Webb, B.-J. M.
Lawrence, Charles E.
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https://doi.org/10.1093/nar/30.5.1268Metadata
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Webb, B.-J. M. 2002. “BALSA: Bayesian Algorithm for Local Sequence Alignment.” Nucleic Acids Research 30 (5) (March 1): 1268–1277. doi:10.1093/nar/30.5.1268.Abstract
The Smith–Waterman algorithm yields a single alignment, which, albeit optimal, can be strongly affected by the choice of the scoring matrix and the gap penalties. Additionally, the scores obtained are dependent upon the lengths of the aligned sequences, requiring a post-analysis conversion. To overcome some of these shortcomings, we developed a Bayesian algorithm for local sequence alignment (BALSA), that takes into account the uncertainty associated with all unknown variables by incorporating in its forward sums a series of scoring matrices, gap parameters and all possible alignments. The algorithm can return both the joint and the marginal optimal alignments, samples of alignments drawn from the posterior distribution and the posterior probabilities of gap penalties and scoring matrices. Furthermore, it automatically adjusts for variations in sequence lengths. BALSA was compared with SSEARCH, to date the best performing dynamic programming algorithm in the detection of structural neighbors. Using the SCOP databases PDB40D-B and PDB90D-B, BALSA detected 19.8 and 41.3% of remote homologs whereas SSEARCH detected 18.4 and 38% at an error rate of 1% errors per query over the databases, respectively.Other Sources
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC101229/Terms of Use
This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAACitable link to this page
http://nrs.harvard.edu/urn-3:HUL.InstRepos:27002730
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