Logic Programming and Nonmonotonic Reasoning

Volume 5753 of the series Lecture Notes in Computer Science pp 573-578

HAPLO-ASP: Haplotype Inference Using Answer Set Programming

  • Esra ErdemAffiliated withFaculty of Engineering and Natural Sciences, Sabancı University
  • , Ozan ErdemAffiliated withFaculty of Engineering and Natural Sciences, Sabancı University
  • , Ferhan TüreAffiliated withDepartment of Computer Science, University of Maryland

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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.