In this paper we present a more efficient algorithm for comparison of minisatellites which has complexity O(n′~3 + m′~3 + mn′~2 + nm′~2 + mn) where n and m are the lengths of the maps and n′ and m′ are the sizes of run-length encoded maps. We show that this algorithm makes a significant improvement for the real biological data, dividing the computing time by a factor 30 on a significant set of data.
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