Approximate string-matching with a single gap for sequence alignment

This paper deals with the approximate string-matching problem with Hamming distance and a single gap for sequence alignment. We consider an extension of the approximate string-matching problem with Hamming distance, by also allowing the existence of a single gap, either in the text, or in the pattern. This problem is strongly and directly motivated by the next-generation re-sequencing procedure. We present a general algorithm that requires O (nm) time, where n is the length of the text and m is the length of the pattern, but this can be reduced to O (mβ) time, if the maximum length β of the gap is given.