Weighted Degenerated Approximate Pattern Matching

We present a bit-parallel approach to degenerated approximate pattern matching problem. That is the problem of finding approximate matches of a “special” pattern in a text of degenerate symbols. The special pattern P = s1 ∗ (a1,b1) . . . sl ∗ (al,bl) sl+1 ∗ (al+1,bl+1) . . . sω, such that symbol ∗ (a,b) is a sequence of at most b but at least a “don’t care” 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 sl 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.