HGM2002 Poster Abstracts: 1. Genome Informatics and Annotation
POSTER NO: 72
An Improved Alignment Algorithm
1Min Zhang, 2Junhua Zhang
The algorithm of Smith & Waterman for identification of maximally similar subsequences is extended to allow identification the global similarity of two sequences. The score matrix is calculated by substitution scores BLOSUM62 and a cost of a+b*k for gaps of length k. The maximally similar subsequences are given by the algorithm of Smith-Waterman, and then the algorithm is invoked recursively to the remnant subsequences until the left and right ends just like the middle order of tree. The score matrix of left subsequence need not be computed, but the right one needs to be.
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