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Approximating the number of Double Cut-and-Join scenarios

Istvan Miklos 1 Eric Tannier 2, 3 
2 BEAGLE - Artificial Evolution and Computational Biology
LIRIS - Laboratoire d'InfoRmatique en Image et Systèmes d'information, Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
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.
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Submitted on : Monday, May 21, 2012 - 11:33:27 AM
Last modification on : Tuesday, October 25, 2022 - 4:16:34 PM

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Istvan Miklos, Eric Tannier. Approximating the number of Double Cut-and-Join scenarios. Theoretical Computer Science, 2012, 439, pp.30-40. ⟨10.1016/j.tcs.2012.03.006⟩. ⟨hal-00699567⟩



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