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.

• Type: Journal
• Year: 2002
• Where: IJFCS
• Authors: Anne Bergeron, Sylvie Hamel
• Keywords: Algorithms, IJFCS 2002, Output Vector, Vector Algorithms