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.