HAPLO-ASP: Haplotype Inference Using Answer Set Programming

Authors:
Esra Erdem;Ozan Erdem;Ferhan Türe
Affiliations:
Faculty of Engineering and Natural Sciences, Sabancı University, Istanbul, Turkey 34956;Faculty of Engineering and Natural Sciences, Sabancı University, Istanbul, Turkey 34956;Department of Computer Science, University of Maryland, USA 20742
Venue:
LPNMR '09 Proceedings of the 10th International Conference on Logic Programming and Nonmonotonic Reasoning
Year:
2009

Citing 7
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Abstract

Identifying maternal and paternal inheritance is essential to be able to find the set of genes responsible for a particular disease. However, due to technological limitations, we have access to genotype data (genetic makeup of an individual), and determining haplotypes (genetic makeup of the parents) experimentally is a costly and time consuming procedure. With these biological motivations, we study haplotype inference--determining the haplotypes that form a given set of genotypes--using Answer Set Programming; we call our approach Haplo-ASP . This note summarizes the range of problems that can be handled by Haplo-ASP , and its applicability and effectiveness on real data in comparison with the other existing approaches.