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The authors explain the problem of local alignment, which is finding pairs of similar subsequences with gaps. The problem exists in biosequence databases. BLAST is a typical software for finding local alignment based on heuristic, but could miss results. A recent exact approach BWT-SW improves the complexity of the Smith-Waterman algorithm under constraints, but still much slower than BLAST. This paper takes on the challenge of designing an accurate and efficient algorithm for evaluating local-alignment searches, especially for long queries. In this paper, they propose an efficient software called ALAE to speed up BWT-SW using a compressed suffix array. ALAE utilizes a family of filtering techniques to prune meaningless calculations and an algorithm for reusing score calculations.
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