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Constraint Programming Models for Transposition Distance Problem

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Advances in Bioinformatics and Computational Biology (BSB 2009)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 5676))

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Abstract

Genome Rearrangements addresses the problem of finding the minimum number of global operations, such as transpositions, reversals, fusions and fissions that transform a given genome into another. In this paper we deal with transposition events, which are events that change the position of two contiguous block of genes in the same chromosome. The transposition event generates the transposition distance problem, that is to find the minimum number of transposition that transform one genome (or chromosome) into another. Although some tractables instances were found [20,14], it is not known if an exact polynomial time algorithm exists. Recently, Dias and Souza [9] proposed polynomial-sized Integer Linear Programming (ILP) models for rearrangement distance problems where events are restricted to reversals, transpositions or a combination of both. In this work we devise a slight different approach. We present some Constraint Logic Programming (CLP) models for transposition distance based on known bounds to the problem.

This work is partially sponsored by CNPq (472504/2007-0 and 479207/2007-0) and FAPESP (2007/05574-4).

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Authors and Affiliations

  1. Institute of Computing - Unicamp - Campinas - SP, Brazil

    Ulisses Dias & Zanoni Dias

Authors
  1. Ulisses Dias
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  2. Zanoni Dias
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Editor information

Editors and Affiliations

  1. Center of Informatics, Av. Prof. Luiz Freire, Federal University of Pernambuco, s/n, Cidade Universitária, PE 50740-540, Recife, Brazil

    Katia S. Guimarães

  2. National Library of Medicine, National Institutes of Health, National Center for Biotechnology Information, 8600 Rockville Pike, Building 38A 8S814, Bethesda, MD 20894, USA

    Anna Panchenko

  3. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Building 38A 8S814, MD 20894,, Bethesda, USA

    Teresa M. Przytycka

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© 2009 Springer-Verlag Berlin Heidelberg

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Dias, U., Dias, Z. (2009). Constraint Programming Models for Transposition Distance Problem. In: Guimarães, K.S., Panchenko, A., Przytycka, T.M. (eds) Advances in Bioinformatics and Computational Biology. BSB 2009. Lecture Notes in Computer Science(), vol 5676. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-03223-3_2

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  • DOI: https://doi.org/10.1007/978-3-642-03223-3_2

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-03222-6

  • Online ISBN: 978-3-642-03223-3

  • eBook Packages: Computer ScienceComputer Science (R0)

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