Approximating the number of Double Cut-and-Join scenarios

Miklós, István and Tannier, E (2012) Approximating the number of Double Cut-and-Join scenarios. THEORETICAL COMPUTER SCIENCE, 439. pp. 30-40. ISSN 0304-3975 10.1016/j.tcs.2012.03.006

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Abstract

The huge number of solutions in genome rearrangement problems calls for algorithms for counting and sampling in the space of solutions, rather than drawing one arbitrary scenario. A closed formula exists for counting the number of DCJ scenarios between co-tailed genomes, but no polynomial result has been published so far for arbitrary genomes. We prove here that it admits a Fully Polynomial time Randomized Approximation Scheme. We use an MCMC almost uniform sampler and prove that it converges to the uniform distribution in fully polynomial time. The MCMC can be used to quickly draw a sample of DCJ scenarios from a prescribed distribution and test some hypotheses on genome evolution. © 2012 Elsevier B.V. All rights reserved.

Item Type: ISI Article
Uncontrolled Keywords: GENES, Polynomial approximation, Genome rearrangements, MCMC, genome rearrangement, FPRAS, DCJ, Comparative genomics
Subjects: Q Science > QA Mathematics and Computer Science > QA75 Electronic computers. Computer science / számítástechnika, számítógéptudomány
Divisions: Informatics Laboratory
Depositing User: EPrints Admin
Date Deposited: 16 Jan 2014 10:31
Last Modified: 05 Feb 2014 12:27
URI: http://eprints.sztaki.hu/id/eprint/7422

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