HAPLO-ASP: Haplotype Inference Using Answer Set Programming

  • Esra Erdem
  • Ozan Erdem
  • Ferhan Türe
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5753)

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.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Esra Erdem
    • 1
  • Ozan Erdem
    • 1
  • Ferhan Türe
    • 2
  1. 1.Faculty of Engineering and Natural SciencesSabancı UniversityIstanbulTurkey
  2. 2.Department of Computer ScienceUniversity of MarylandUSA

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