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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

Linearization of ancestral multichromosomal genomes

Ján Maňuch12, Murray Patterson34*, Roland Wittler5, Cedric Chauve1 and Eric Tannier34*

Author Affiliations

1 Department of Mathematics, Simon Fraser University, Burnaby BC, V5A1S6, Canada

2 Department of Computer Science, University of British Columbia, Vancouver BC, V6T1Z4, Canada

3 INRIA Rhône-Alpes, 655 avenue de I'Europe, F-38344 Montbonnot, France

4 Laboratoire de Biométrie et Biologie Évolutive, CNRS and Université de Lyon 1, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne, France

5 Genome Informatics, Faculty of Technology and Institute for Bioinformatics, Center for Biotechnology (CeBiTec), Bielefeld University, 33594 Bielefeld, Germany

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BMC Bioinformatics 2012, 13(Suppl 19):S11  doi:10.1186/1471-2105-13-S19-S11

Published: 19 December 2012

Abstract

Background

Recovering the structure of ancestral genomes can be formalized in terms of properties of binary matrices such as the Consecutive-Ones Property (C1P). The Linearization Problem asks to extract, from a given binary matrix, a maximum weight subset of rows that satisfies such a property. This problem is in general intractable, and in particular if the ancestral genome is expected to contain only linear chromosomes or a unique circular chromosome. In the present work, we consider a relaxation of this problem, which allows ancestral genomes that can contain several chromosomes, each either linear or circular.

Result

We show that, when restricted to binary matrices of degree two, which correspond to adjacencies, the genomic characters used in most ancestral genome reconstruction methods, this relaxed version of the Linearization Problem is polynomially solvable using a reduction to a matching problem. This result holds in the more general case where columns have bounded multiplicity, which models possibly duplicated ancestral genes. We also prove that for matrices with rows of degrees 2 and 3, without multiplicity and without weights on the rows, the problem is NP-complete, thus tracing sharp tractability boundaries.

Conclusion

As it happened for the breakpoint median problem, also used in ancestral genome reconstruction, relaxing the definition of a genome turns an intractable problem into a tractable one. The relaxation is adapted to some biological contexts, such as bacterial genomes with several replicons, possibly partially assembled. Algorithms can also be used as heuristics for hard variants. More generally, this work opens a way to better understand linearization results for ancestral genome structure inference.