HAPLOTYPE BLOCK PARTITIONING AND TAG SNP SELECTION UNDER THE PERFECT PHYLOGENY MODEL

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ESLAHCHI CHANGIZ; KATANFOROUSH ALI; PEZESHK HAMID; AFZALY NARJES

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Journal: Iranian Journal of Biotechnology Year:2011 | Volume:9 | Issue:4 Page(s): 281-289

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Information Journal Paper

Title

HAPLOTYPE BLOCK PARTITIONING AND TAG SNP SELECTION UNDER THE PERFECT PHYLOGENY MODEL

Author(s)

ESLAHCHI CHANGIZ | KATANFOROUSH ALI | PEZESHK HAMID | AFZALY NARJES | Issue Writer Certificate

Keywords

SINGLE NUCLEOTIDE POLYMORPHISMSQ2

HAPLOTYPEQ2

TAGSNPQ2

PERFECT PHYLOGENYQ2

Abstract

SINGLE NUCLEOTIDE POLYMORPHISMS (SNPs) are the most usual form of polymorphism in human genome.Analyses of genetic variations have revealed that individual genomes share common SNP-haplotypes. The particular pattern of these common variations forms a block-like structure on human genome. In this work, we develop a new method based on the PERFECT PHYLOGENY Model to identify HAPLOTYPE blocks using samples of individual genomes. We introduce a rigorous definition of the quality of the partitioning of HAPLOTYPEs into blocks and devise a greedy algorithm for finding the proper partitioning in case of perfect and semi-perfect phylogeny. It is shown that the minimum number of tag SNPs in a HAPLOTYPE block of PERFECT PHYLOGENY can be obtained by a polynomial time algorithm.We compare the performance of our algorithm on HAPLOTYPE data of human chromosome 21 with other previously developed methods through simulations.The results demonstrate that our algorithm outperforms the conventional implementation of the Four Gamete Test approach which is the only available method for HAPLOTYPE block partitioning based on PERFECT PHYLOGENY.

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APA: Copy

ESLAHCHI, CHANGIZ, KATANFOROUSH, ALI, PEZESHK, HAMID, & AFZALY, NARJES. (2011). HAPLOTYPE BLOCK PARTITIONING AND TAG SNP SELECTION UNDER THE PERFECT PHYLOGENY MODEL. IRANIAN JOURNAL OF BIOTECHNOLOGY, 9(4), 281-289. SID. https://sid.ir/paper/139340/en

Vancouver: Copy

ESLAHCHI CHANGIZ, KATANFOROUSH ALI, PEZESHK HAMID, AFZALY NARJES. HAPLOTYPE BLOCK PARTITIONING AND TAG SNP SELECTION UNDER THE PERFECT PHYLOGENY MODEL. IRANIAN JOURNAL OF BIOTECHNOLOGY[Internet]. 2011;9(4):281-289. Available from: https://sid.ir/paper/139340/en

IEEE: Copy

CHANGIZ ESLAHCHI, ALI KATANFOROUSH, HAMID PEZESHK, and NARJES AFZALY, “HAPLOTYPE BLOCK PARTITIONING AND TAG SNP SELECTION UNDER THE PERFECT PHYLOGENY MODEL,” IRANIAN JOURNAL OF BIOTECHNOLOGY, vol. 9, no. 4, pp. 281–289, 2011, [Online]. Available: https://sid.ir/paper/139340/en

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