TY - GEN
T1 - Computational experiments on algorithms for haplotype inference problems by pure parsimony
AU - Wang, I. Lin
AU - Yang, Hui E.
PY - 2006
Y1 - 2006
N2 - To analyze the function of DNA, researchers have to obtain each haplotype, the genetic constitution of an individual chromosome, of an individual for analysis. Due to the significant efforts required in collecting haplotypes, the descriptions of one conflated pair of haplotypes called genotypes are usually collected. Since the genotype data contains insufficient information to identify the combination of DNA sequence in each copy of a chromosome, one has to solve the population haplotype inference problem by pure parsimony criterion which uses the minimum number of haplotypes to infer the haplotype data from genotype data for a population. Previous researches use mathematical programming methods such as integer programming and semidefinite programming models to solve the population haplotype inference problem. However, no computational experiment has ever been conducted to evaluate the algorithmic effectiveness. This paper thus conducts the first computational experiments on four haplotyping algorithms, including our new greedy heuristic and three pervious haplotyping algorithms.
AB - To analyze the function of DNA, researchers have to obtain each haplotype, the genetic constitution of an individual chromosome, of an individual for analysis. Due to the significant efforts required in collecting haplotypes, the descriptions of one conflated pair of haplotypes called genotypes are usually collected. Since the genotype data contains insufficient information to identify the combination of DNA sequence in each copy of a chromosome, one has to solve the population haplotype inference problem by pure parsimony criterion which uses the minimum number of haplotypes to infer the haplotype data from genotype data for a population. Previous researches use mathematical programming methods such as integer programming and semidefinite programming models to solve the population haplotype inference problem. However, no computational experiment has ever been conducted to evaluate the algorithmic effectiveness. This paper thus conducts the first computational experiments on four haplotyping algorithms, including our new greedy heuristic and three pervious haplotyping algorithms.
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U2 - 10.2991/jcis.2006.243
DO - 10.2991/jcis.2006.243
M3 - Conference contribution
AN - SCOPUS:33847737298
SN - 9078677015
SN - 9789078677017
T3 - Proceedings of the 9th Joint Conference on Information Sciences, JCIS 2006
BT - Proceedings of the 9th Joint Conference on Information Sciences, JCIS 2006
T2 - 9th Joint Conference on Information Sciences, JCIS 2006
Y2 - 8 October 2006 through 11 October 2006
ER -