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Bioinformatics Advance Access originally published online on February 26, 2004
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Bioinformatics 20(12) © Oxford University Press 2004; all rights reserved.

Haplotypes histories as pathways of recombinations

Nadia El-Mabrouk 1,* and Damian Labuda 2

1 Département d'informatique et de recherche opérationnelle, Université de Montréal, CP 6128 Succursale Centre-ville, Montréal, QC, Canada H3C 3J7 and 2 Centre de recherche, Hopital Sainte-Justine, Département de Pédiatrie, Université de Montréal, 3175 Côte-Sainte-Catherine, Montréal, QC, Canada H3T 1C5

Received on April 21, 2003; revised on September 8, 2003; accepted on September 9, 2003
Advance Access Publication February 26, 2004

Motivation: The diversity of a haplotype, represented as a string of polymorphic sites along a DNA sequence, increases exponentially with the number of sites if recombinations are taking place. Reconstructing the history of recombinations compared with that of the polymorphic sites is thus extremely difficult. However, in the human genome, because of the relatively simple pattern of haplotype diversity dominated by a few ancestral haplotypes, the complexity of the recombinational network can be reduced, thus making its reconstruction feasible. We focus on the problem of inferring the recombination pathways starting with putative ancestral haplotypes and leading to new rare recombinant haplotypes.

Results: We describe classes of recombinations that represent the whole set of minimal recombination pathways leading to a new haplotype. We present an O(n2) algorithm that outputs such representative recombination pathways. We apply it to haplotypes of the 8 kb dystrophin gene segment dys44.

Availability: A software implementing the algorithm and some other extentions has been developed on a Java platform (JDK 1.3.1). It is freely available at http://www.iro.umontreal.ca/~mabrouk/

Contact: mabrouk{at}iro.umontreal.ca

* To whom correspondence should be addressed.


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