BWT-SW is a local alignment tool for searching nucleotide sequences. It performs the same function as BLASTn, the BLAST program for finding regions of local similarity between nucleotide sequences. While BLAST is an approximation of the Smith-Waterman local alignment algorithm and may miss significant alignments , BWT-SW finds all local alignments1. The running speed of BWT-SW depends on the lengths of the database sequence and the query sequence. On a set of experiments using human genome as the database sequence, BWT-SW takes the same order of time as BLASTn on query sequences of length 1000 nucleotides or less . As far as we know, BWT-SW is the first practical tool that can find all local alignments.
C.K. Wong (email@example.com)
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T.W. Lam; W.K. Sung; S.L. Tam; C.K. Wong; S.M. Yiu.
Compressed Indexing and Local Alignment of DNA
Bioinformatics 2008; doi: 10.1093/bioinformatics/btn032