DocumentCode :
2043362
Title :
A message passing algorithm for haplotype assembly
Author :
Puljiz, Zrinka ; Vikalo, Haris
Author_Institution :
Dept. of Electr. & Comput. Eng., Univ. of Texas at Austin, Austin, TX, USA
fYear :
2013
fDate :
3-6 Nov. 2013
Firstpage :
1726
Lastpage :
1729
Abstract :
Homologous chromosome pairs have similar DNA sequences and encode the same type of information but are not identical. The most common form of variations between them are the so-called single nucleotide polymorphisms (SNPs), where two chromosomes in a homologous pair differ at individual corresponding positions. The problem of haplotype assembly is concerned with finding an ordered sequence of SNPs associated with each one of the chromosomes in a pair. The information about genetic variations (i.e., SNPs) is inferred using short reads provided by the high-throughput DNA sequencing systems. The reads are potentially erroneous and haplotype assembly can thus be interpreted as the process of separating fragments into two potentially inconsistent (due to noise) classes, each corresponding to one of the haplotypes in a pair. Solving this problem is known to be NP-hard, and hence practical haplotype assembly typically involves heuristics and low complexity approximations. In our work, we propose novel graphical models of the hap-lotype assembly problem and design efficient message passing algorithms for solving it. The developed algorithms perform close to the existing state-of-the-art techniques while being more computationally efficient.
Keywords :
DNA; biology computing; computational complexity; genetics; graph theory; message passing; DNA sequence; NP-hard problem; genetic variation; graphical model; hap-lotype assembly problem; high throughput DNA sequencing system; homologous chromosome pair; message passing algorithm; practical haplotype assembly; single nucleotide polymorphism; Approximation algorithms; Assembly; Biological cells; DNA; Genomics; Graphical models; Sequential analysis;
fLanguage :
English
Publisher :
ieee
Conference_Titel :
Signals, Systems and Computers, 2013 Asilomar Conference on
Conference_Location :
Pacific Grove, CA
Print_ISBN :
978-1-4799-2388-5
Type :
conf
DOI :
10.1109/ACSSC.2013.6810596
Filename :
6810596
Link To Document :
بازگشت