Pseudo-Boolean Programming for Partially Ordered Genomes

Abstract : Comparing genomes of different species is a crucial problem in comparative genomics. Different measures have been proposed to compare two genomes: number of common intervals, number of adjacencies, number of reversals, etc. These measures are classically used between two totally ordered genomes. However, genetic mapping techniques often give rise to different maps with some unordered genes. Starting from a partial order between genes of a genome, one method to find a total order consists in optimizing a given measure between a linear extension of this partial order and a given total order of a close and well-known genome. However, for most common measures, the problem turns out to be NP-hard. In this paper, we propose a (0, 1)-linear programming approach to compute a linear extension of one genome that maximizes the number of common intervals (resp. the number of adjacencies) between this linear extension and a given total order. Next, we propose an algorithm to find linear extensions of two partial orders that maximize the number of adjacencies.
Liste complète des métadonnées

Cited literature [9 references]  Display  Hide  Download

https://hal.archives-ouvertes.fr/hal-00416458
Contributor : Guillaume Fertin <>
Submitted on : Monday, September 14, 2009 - 11:46:05 AM
Last modification on : Wednesday, May 23, 2018 - 3:44:02 PM
Document(s) archivé(s) le : Tuesday, June 15, 2010 - 11:37:55 PM

File

RECOMB-CG2009.pdf
Files produced by the author(s)

Identifiers

Citation

Sébastien Angibaud, Guillaume Fertin, Annelyse Thevenin, Stéphane Vialette. Pseudo-Boolean Programming for Partially Ordered Genomes. RECOMB-CG 2009, Sep 2009, Budapest, Hungary. pp.126-137, ⟨10.1007/978-3-642-04744-2_11⟩. ⟨hal-00416458⟩

Share

Metrics

Record views

793

Files downloads

103