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OPTIMAL SOLUTION TO HAPLOTYPE INFERENCE USING PARSIMONY MODEL

PHATAK, MUKTA
http://rave.ohiolink.edu/etdc/view?acc_num=ucin1092940172

Abstract Details

2004, MS, University of Cincinnati, Engineering : Computer Science.
Haplotyping is considered as one of the important areas in the Post-Genome research. It is essential to know the haplotype information to associate a certain disease to the specific region on chromosome. With the current sequencing technology, determination of a haplotype is costly and difficult. This leaves us with the task of inferring haplotypes from the genotype data which instead is easily available. For a genotype with n heterozygous sites, there are 2 n-1 number of haplotypes possible. The problem of inferring haplotypes becomes combinatorially very large and it would be impossible to compute it without the use of any genetic model. We have used parsimonious approach in junction with Clark's inferal method to infer haplotypes for a set of genotypes. The objective is to find the fewest possible distinct haplotypes while trying to resolve all genotypes of the input genotype data. Hubbell [7] proved that this version of the problem is NP hard. Hence we have come up with the heuristic to solve the same. Our algorithm does not expand all the possibilities of each genotype and hence does not get computationally expensive. It tries to find the optimal solution given the set of genotype data. We observed that for the data with low recombination, the algorithm works efficiently. Since we consider the Parsimony Model, the accuracy drops with the increasing recombination factor.
Dr. Yizong Cheng (Advisor)
Computer Science

Recommended Citations

Citations

  • PHATAK, M. (2004). OPTIMAL SOLUTION TO HAPLOTYPE INFERENCE USING PARSIMONY MODEL [Master's thesis, University of Cincinnati]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1092940172

    APA Style (7th edition)

  • PHATAK, MUKTA. OPTIMAL SOLUTION TO HAPLOTYPE INFERENCE USING PARSIMONY MODEL. 2004. University of Cincinnati, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=ucin1092940172.

    MLA Style (8th edition)

  • PHATAK, MUKTA. "OPTIMAL SOLUTION TO HAPLOTYPE INFERENCE USING PARSIMONY MODEL." Master's thesis, University of Cincinnati, 2004. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1092940172

    Chicago Manual of Style (17th edition)

ucin1092940172
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© 2004, all rights reserved.
This open access ETD is published by University of Cincinnati and OhioLINK.