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Weighted Degenerated Approximate Pattern Matching β
Abstract. We present a bit-parallel approach to degenerated approximate pattern matching problem. That is the problem of finding approximate matches of a βspecial β pattern in a text of degenerate symbols. The special pattern P = s1 β (a1,b1)... sβ β (a β,b β) sβ+1 β (a β+1,b β+1)... sΟ, such that symbol β (a,b) is a sequence of at most b but at least a βdonβt care β symbols which match any symbol within the alphabet, i.e. a sequence of subpatterns with gaps; the pattern is associated with integer weights in each subpattern sβ for replacements, insertions, and deletions. The problem is to match the pattern such that the minimum sum of weights is achieved. The total time complexity is (k(log(k+2)+1)mn)/w, where m is the length of the pattern P, n is the length of text of degenerate symbols, k is the maximum number of edit operations performed, and w is the length of the computer word