A Fast and Simple Pattern Matching with Hamming Distance on Large Alphabets
Strahil Ristov · Journal of Computational Biology · 2016
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.