Recovering haplotype structure through recombination and gene conversion

Lajoie, Mathieu and El-Mabrouk, Nadia (2005). Recovering haplotype structure through recombination and gene conversion. In: Roderic Guigó, Federico Morán, Alfonso Valencia and Josep F. Abril, ECCB/JBI'05 proceedings. Joint Meeting of the 4th European Conference on Computational Biology/6th Meeting of the Spanish Bioinformatics Network, Madrid, Spain, (173-179). 28 September - 1October 2005. doi:10.1093/bioinformatics/bti1128


Author Lajoie, Mathieu
El-Mabrouk, Nadia
Title of paper Recovering haplotype structure through recombination and gene conversion
Conference name Joint Meeting of the 4th European Conference on Computational Biology/6th Meeting of the Spanish Bioinformatics Network
Conference location Madrid, Spain
Conference dates 28 September - 1October 2005
Proceedings title ECCB/JBI'05 proceedings   Check publisher's open access policy
Journal name Bioinformatics   Check publisher's open access policy
Place of Publication Oxford, United Kingdom
Publisher Oxford University Press
Publication Year 2005
Sub-type Fully published paper
DOI 10.1093/bioinformatics/bti1128
ISSN 1367-4803
1367-4811
Editor Roderic Guigó
Federico Morán
Alfonso Valencia
Josep F. Abril
Volume 21
Issue suppl 2
Start page 173
End page 179
Total pages 6
Language eng
Formatted Abstract/Summary
Motivation: Understanding haplotype evolution subject to mutation, recombination and gene conversion is fundamental to understand genetic specificities of human populations and hereditary bases of complex disorders. The goal of this project is to develop new algorithmic tools assisting the reconstruction of historical relationships between haplotypes and the inference of haplotypes from genotypes.
Results: We present two new algorithms. The first one finds an optimal pathway of mutations, recombinations and gene conversions leading to a given haplotype of size m from a population of h haplotypes. It runs in time O(mhs2), where s is the maximum number of contiguous sites that can be exchanged in a single gene conversion. The second one finds an optimal pathway of mutations and recombinations leading to a given genotype, and runs in time O(mh2). Both algorithms are based on a penalty score model and use a dynamic programming approach. We apply the second one to the problem of inferring haplotypes from genotypes, and show how it can be used as an independent tool, or to improve the performance of existing methods.
Availability: The algorithms have been implemented in JAVA and are available on request.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Conference Paper
Collection: Institute for Molecular Bioscience - Publications
 
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Created: Wed, 25 Jul 2012, 11:21:39 EST by Susan Allen on behalf of Institute for Molecular Bioscience