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Background  Mancheron, Uricaru and Rivals ( Nucleic Acids Res . 39:e101, 2011) recently introduced a new approach in the context of multiple genome comparison that allows to detect regions of strong overlaps in a set of pairwise local alignments between several reference genomes and one target genome. Such overlap regions are an important source of information in genome annotation.    Results  In this paper we introduce a series of algorithms that improve over the approach of Mancheron  et al ., both in terms of computational complexity and in practical runtime. We also extend the problem definition such that overlaps to different reference genomes can be rated differently and regions overlapping only a subset of the reference genomes are detected.

Multiple genome comparison based on overlap regions of pairwise local alignments