Algorithm for haplotype inferring via galled-tree networks with simple galls

Authors:
Arvind Gupta;Ján Maňuch;Ladislav Stacho;Xiaohong Zhao
Affiliations:
School of Computing Science and Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada;School of Computing Science and Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada;School of Computing Science and Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada;School of Computing Science and Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
Venue:
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
Year:
2007

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Abstract

The problem of determining haplotypes from genotypes has gained considerable prominence in the research community. Here the focus is on determining sets of SNP values on individual chromosomes since such information captures the genetic causes of diseases. Present algorithmic tools for haplotyping make effective use of phylogenetic trees. Here the underlying assumption is that recombinations are not present, an assumption based on experimental results. However these results do not fully exclude recombinations and models are needed that incorporate this extra degree of complication. Recently, Gusfield studied the two cases: haplotyping via imperfect phylogenies with a single homoplasy and via galled-tree networks with one gall. In earlier work we characterized the existence of the galled-tree networks. Building on this, we present a polynomial algorithm for haplotyping via galled-tree networks with simple galls (having two mutations). In the end, we give the experimental results comparing our algorithm with PHASE on simulated data.