A Fast and Simple Pattern Matching with Hamming Distance on Large Alphabets.
We present a fast method for calculation of Hamming distance vector based on a simple preprocessing of the target text. For applications on protein sequences, with alphabet of 20 symbols or more, the proposed method is an order of magnitude faster than the brute force approach while much simpler than previously published methods.
Department of Electronics, Ruđer Bošković Institute , Zagreb, Croatia .
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Ristov
D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D011506:Proteins / Q000235:genetics*
D011506:Proteins
Hamming distance; approximate pattern matching; protein search.