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Haplotype Inference Using Propositional Satisfiability

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Mathematical Approaches to Polymer Sequence Analysis and Related Problems

Abstract

Haplotype inference is an important problem in computational biology, which has deserved large effort and attention in the recent years. Haplotypes encode the genetic data of an individual at a single chromosome. However, humans are diploid (chromosomes have maternal and paternal origin), and it is technologically infeasible to separate the information from homologous chromosomes. Hence, mathematical methods are required to solve the haplotype inference problem. A relevant approach is the pure parsimony. The haplotype inference by pure parsimony (HIPP) aims at finding the minimum number of haplotypes which explains a given set of genotypes. This problem is NP-hard. Boolean satisfiability (SAT) has successful applications in several fields. The use of SAT-based techniques with pure parsimony haplotyping has shown to produce very efficient results. This chapter describes the haplotype inference problem and the SAT-based models developed to solve the problem. Experimental results confirm that the SAT-based methods represent the state of the art in the field of HIPP.

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Notes

  1. 1.

    http://www.ncbi.nlm.nih.gov/projects/SNP

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Acknowledgments

This research was funded by Fundação para a Ciência e Tecnologia under research project SHIPs (PTDC/EIA/64164/2006) and PhD grant (SFRH/BD/28599/2006), and by Microsoft under contract 2007-017 of the Microsoft Research PhD Scholarship Programme.

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Authors and Affiliations

  1. IST/INESC-ID, Technical University of Lisbon, R. Alves Redol 9, 1000-029, Lisboa, Portugal

    Ana Graça

Authors
  1. Ana Graça
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  2. João Marques-Silva
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  3. Inês Lynce
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Corresponding author

Correspondence to Ana Graça .

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Editors and Affiliations

  1. Dipto. Informatica e Sistemistica, Università Roma, La Sapienza, Via Ariosto 25, Roma, 00185, Italy

    Renato Bruni

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Graça, A., Marques-Silva, J., Lynce, I. (2011). Haplotype Inference Using Propositional Satisfiability. In: Bruni, R. (eds) Mathematical Approaches to Polymer Sequence Analysis and Related Problems. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-6800-5_7

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