Fast calculation of a segment mutation distance between long sequences

BpMatch is a new algorithm whose function is to efficiently calculate, from sequences S and T, the maximum coverage of T using only subsequences and complemented reversed subsequences of S, with minimum length l, possibly overlapped, and, in such a maximum coverage, to minimize the number of subsequences used. The problem is solved by executing a preelaboration of S (independently from the sequence on which a maximum coverage will be later looked for, and therefore executed only once for any target sequence T), generating a graph which allows a fast recognizing of S's subsequences. Graphs G and G' must be generated from S and complemented reversed S, then, using G, G' and T, calculus of the maximum coverage can be computed in linear space and time.