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Bioinformatics Advance Access originally published online on April 28, 2009
Bioinformatics 2009 25(14):1833-1835; doi:10.1093/bioinformatics/btp285
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

baobabLUNA: the solution space of sorting by reversals

Marília D. V. Braga {dagger}

Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS UMR5558; Inria Grenoble Rhône-Alpes, Lyon, France


  Abstract

Summary: Computing the reversal distance and searching for an optimal sequence of reversals to transform a unichromosomal genome into another are useful algorithmic tools to analyse real evolutionary scenarios. Currently, these problems can be solved by at least two available softwares, the prominent of which are GRAPPA and GRIMM. However, the number of different optimal sequences is usually huge and taking only the distance and/or one example is often insufficient to do a proper analysis. Here, we offer an alternative and present baobabLUNA, a framework that contains an algorithm to give a compact representation of the whole space of solutions for the sorting by reversals problem.

Availability and Implementation: Compiled code implemented in Java is freely available for download at http://pbil.univ-lyon1.fr/software/luna/. Documentation with methodological background, technical aspects, download and setup instructions, interface description and tutorial are available at http://pbil.univ-lyon1.fr/software/luna/doc/luna-doc.pdf.

Contact: mdvbraga{at}gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.

{dagger} Present address: Universität Bielefeld Technische Fakultät AG Genominformatik, Postfach 10 01 31, 33501 Bielefeld, Germany

Associate Editor: Alex Bateman

Received on February 19, 2009; revised on April 21, 2009; accepted on April 22, 2009

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