Methodology article
Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments
1 Bioinformatics Program and Chemistry Department, Saint Vincent College, Latrobe, PA 15650 USA
2 Department of Medicine, University of California, San Diego, La Jolla, CA 92093 USA
3 Department of Systems and Information Engineering, University of Virginia, Charlottesville, VA 22908 USA
4 Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908 USA
BMC Bioinformatics 2010, 11:146 doi:10.1186/1471-2105-11-146
Published: 22 March 2010Additional files
Additional file 1:
Counts of suboptimal Zuker alignments sampled. Maximum and minimum number of suboptimal alignments produced for each sequence pair, for the neighborhoods with alignment scores within the indicated percent of the optimal score. Each neighborhood had six different combinations of scoring matrix and gap penalties.
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Additional file 2:
List of CATH domains used in the study. The table lists the pair numbering used throughout the paper, the CATH version 3.2 domain names, the expectation value calculated by SSEARCH in a search of a database of 10,000 domains, the percent identity, and the CATH family of the domains.
Format: PDF Size: 72KB Download file
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