HAPLO-ASP: Haplotype inference using answer set programming

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.