An information theoretic viewpoint on haplotype reconstruction from SNP fragments

Chen Huimin, Zhao Zhiyu

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

Abstract

The problem of haplotype reconstruction based on aligned single nucleotide polymorphism (SNP) fragments is formulated as decoding over a discrete memoryless channel. An information theoretic view point is used to illustrate the deficiency of parsimonious models such as minimum error correction model. A new computational model with genotype information is proposed and a low complexity reconstruction algorithm for this model is shown to guarantee the desired reconstruction rate by increasing the number of SNP fragments sequentially. The advantage of using genotype information is quantified by exploiting a simplified statistical model for haplotype sequences.

Original languageEnglish (US)
Title of host publication3rd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2009
DOIs
StatePublished - 2009
Event3rd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2009 - Beijing, China
Duration: Jun 11 2009Jun 13 2009

Other

Other3rd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2009
CountryChina
CityBeijing
Period6/11/096/13/09

Fingerprint

Nucleotides
Polymorphism
Haplotypes
Single Nucleotide Polymorphism
Genotype
Statistical Models
Error correction
Decoding

Keywords

  • Error correction
  • Genotype
  • Haplotype inference
  • Sequential test

ASJC Scopus subject areas

  • Biotechnology
  • Biomedical Engineering

Cite this

Huimin, C., & Zhiyu, Z. (2009). An information theoretic viewpoint on haplotype reconstruction from SNP fragments. In 3rd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2009 [5162329] https://doi.org/10.1109/ICBBE.2009.5162329

An information theoretic viewpoint on haplotype reconstruction from SNP fragments. / Huimin, Chen; Zhiyu, Zhao.

3rd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2009. 2009. 5162329.

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

Huimin, C & Zhiyu, Z 2009, An information theoretic viewpoint on haplotype reconstruction from SNP fragments. in 3rd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2009., 5162329, 3rd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2009, Beijing, China, 6/11/09. https://doi.org/10.1109/ICBBE.2009.5162329
Huimin C, Zhiyu Z. An information theoretic viewpoint on haplotype reconstruction from SNP fragments. In 3rd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2009. 2009. 5162329 https://doi.org/10.1109/ICBBE.2009.5162329
Huimin, Chen ; Zhiyu, Zhao. / An information theoretic viewpoint on haplotype reconstruction from SNP fragments. 3rd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2009. 2009.
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