Computation of median gene clusters

Authors:
Sebastian Böcker;Katharina Jahn;Julia Mixtacki;Jens Stoye
Affiliations:
Institut für Informatik, Friedrich-Schiller-Universität Jena, Germany;International NRW Graduate School in Bioinformatics and Genome Research, Universität Bielefeld, Germany;International NRW Graduate School in Bioinformatics and Genome Research, Universität Bielefeld, Germany;Technische Fakultät, Universität Bielefeld, Germany
Venue:
RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology
Year:
2008

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Abstract

Whole genome comparison based on gene order has become a popular approach in comparative genomics. An important task in this field is the detection of gene clusters, i.e. sets of genes that occur colocalized in several genomes. For most applications it is preferable to extend this definition to allow for small deviations in the gene content of the cluster occurrences. However, relaxing the equality constraint increases the computational complexity of gene cluster detection drastically. Existing approaches deal with this problem by using simplifying constraints on the cluster definition and/or allowing only pairwise genome comparison. In this paper we introduce a cluster concept named median gene clusters that improves over existing models and present efficient algorithms for their computation that allow for the detection of approximate gene clusters in multiple genomes.