Haplotype inference by pure-parsimony using revamped delayed haplotype selection. (c2011)

2011 ◽  
Author(s):  
Raymond Abdallah
Keyword(s):  
Haplotype Inference ◽  
Pure Parsimony

Haplotype Inference by Pure Parsimony: A Survey

2010 ◽  
Vol 17 (8) ◽  
pp. 969-992 ◽  
Author(s):  
Ana Graça ◽  
Inês Lynce ◽  
João Marques-Silva ◽  
Arlindo L. Oliveira
Keyword(s):  
Haplotype Inference ◽  
Pure Parsimony

scholarly journals HAPLOTYPE INFERENCE WITH BOOLEAN SATISFIABILITY

2008 ◽  
Vol 17 (02) ◽  
pp. 355-387 ◽  
Author(s):  
INÊS LYNCE ◽  
JOÃO MARQUES-SILVA
Keyword(s):  
Human Population ◽  
Haplotype Inference ◽  
Genotype Data ◽  
Nucleotide Polymorphisms ◽  
Human Beings ◽  
Single Nucleotide ◽  
Haplotype Data ◽  
Np Hard Problem ◽  
Pure Parsimony ◽  
Parsimony Criterion

Mutation in DNA is the principal cause for differences among human beings, and Single Nucleotide Polymorphisms (SNPs) are the most common mutations. Hence, a fundamental task is to complete a map of haplotypes (which identify SNPs) in the human population. Associated with this effort, a key computational problem is the inference of haplotype data from genotype data, since in practice genotype data rather than haplotype data is usually obtained. Different haplotype inference approaches have been proposed, including the utilization of statistical methods and the utilization of the pure parsimony criterion. The problem of haplotype inference by pure parsimony (HIPP) is interesting not only because of its application to haplotype inference, but also because it is a challenging NP-hard problem, being APX-hard. Recent work has shown that a SAT-based approach is the most efficient approach for the problem of haplotype inference by pure parsimony (HIPP), being several orders of magnitude faster than existing integer linear programming and branch and bound solutions. This paper provides a detailed description of SHIPs, a SAT-based approach for the HIPP problem, and presents comprehensive experimental results comparing SHIPs with all other exact approaches for the HIPP problem. These results confirm that SHIPs is currently the most effective approach for the HIPP problem.

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