Computational experiments on algorithms for haplotype inference problems by pure parsimony

I. Lin Wang, Hui E. Yang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

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.

Original languageEnglish
Title of host publicationProceedings of the 9th Joint Conference on Information Sciences, JCIS 2006
DOIs
Publication statusPublished - 2006
Event9th Joint Conference on Information Sciences, JCIS 2006 - Taiwan, ROC, Taiwan
Duration: 2006 Oct 82006 Oct 11

Publication series

NameProceedings of the 9th Joint Conference on Information Sciences, JCIS 2006
Volume2006

Other

Other9th Joint Conference on Information Sciences, JCIS 2006
CountryTaiwan
CityTaiwan, ROC
Period06-10-0806-10-11

All Science Journal Classification (ASJC) codes

  • Engineering(all)

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