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This article is part of the supplement: Proceedings of the Tenth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics

Open Access Proceedings

Multiple genome comparison based on overlap regions of pairwise local alignments

Katharina Jahn12*, Henner Sudek2 and Jens Stoye2

Author Affiliations

1 Department of Mathematics and Statistics, University of Ottawa, Canada

2 Technische Fakultät, Universität Bielefeld, Germany

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BMC Bioinformatics 2012, 13(Suppl 19):S7  doi:10.1186/1471-2105-13-S19-S7

Published: 19 December 2012



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.


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.