Vector Algorithms for Approximate String Matching

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Vector Algorithms for Approximate String Matching
Vector algorithms allow the computation of an output vector r = r1r2 :::rm given an input vector e = e1e2 :::em in a bounded number of operations, independent of m the length of the vectors. The allowable operations are usually restricted to bit-wise operations available in processors, including shifts and binary addition with carry. These restrictionsimply that the existenceof a vector algorithmfor a particularproblem opens the way to extremelyfast implementations,usingtheinherentparallelismof bit-wiseoperations. This paper presents general results on the existence and construction of vector algorithms, with a particular focus on problems arising from computational biology. We show that e cient vector algorithms exist for the problem of approximate string matching with arbitrary weighted distances, generalizing a previous result by G. Myers. We also characterize a class of automata for which vector algorithms can be automatically derived from the transition table of the automata.
Anne Bergeron, Sylvie Hamel
Added 22 Dec 2010
Updated 22 Dec 2010
Type Journal
Year 2002
Authors Anne Bergeron, Sylvie Hamel
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