Skip Navigation



Bioinformatics Advance Access published online on July 7, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti572
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
21/17/3475    most recent
bti572v2
bti572v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Li, Z.
Right arrow Articles by Chen, L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Li, Z.
Right arrow Articles by Chen, L.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received May 24, 2005
Revised June 30, 2005
Accepted July 4, 2005

Article

A parsimonious tree-grow method for haplotype inference

Zhenping Li 1, Wenfeng Zhou 2, Xiangsun Zhang 3 *, and Luonan Chen 4*

1 Beijing Materials Institute, Beijing 101149, China; Chinese Academy of Sciences, Beijing 100080, China
2 Beijing Materials Institute, Beijing 101149, China
3 Chinese Academy of Sciences, Beijing 100080, China
4 Osaka Sangyo University, Osaka 574-8530, Japan

* To whom correspondence should be addressed.
Luonan Chen, E-mail: chen{at}elec.osaka-sandai.ac.jp


  Abstract

Motivation: Haplotype information has become increasingly important in analyzing fine-scale molecular genetics data, such as disease genes mapping and drug design. Parsimony Haplotyping is one of haplotyping problems belonging to NP-hard class.

Results: In this paper, we aim to develop a novel algorithm for the haplotype inference problem with the parsimony criterion, based on a parsimonious tree-grow method (PTG). PTG is a heuristic algorithm that can find the minimum number of distinct haplotypes based on the criterion of keeping all genotypes resolved during tree-grow process. In addition, a block-partitioning method is also proposed to improve the computational efficiency. We show that the proposed approach is not only effective with a high accuracy but also very efficient with the computational complexity in the order of O(m2n) time for n SNP sites in m individual genotypes.

Availability: The software is available upon request from the authors, or from http://zhangroup.aporc.org/bioinfo/ptg/.

*This author's work is partly supported by Informatics Research Center for Development of Knowledge Society Infrastructure, Graduate School of Informatics, Kyoto University, Japan
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
S. Climer, G. Jager, A. R. Templeton, and W. Zhang
How frugal is mother nature with haplotypes?
Bioinformatics, January 1, 2009; 25(1): 68 - 74.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Y. Zhao, Y. Xu, Z. Wang, H. Zhang, and G. Chen
A better block partition and ligation strategy for individual haplotyping
Bioinformatics, December 1, 2008; 24(23): 2720 - 2725.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Epidemiol. Biomarkers Prev.Home page
K. Allen-Brady, L. A. Cannon-Albright, S. L. Neuhausen, and N. J. Camp
A Role for XRCC4 in Age at Diagnosis and Breast Cancer Risk.
Cancer Epidemiol. Biomarkers Prev., July 1, 2006; 15(7): 1306 - 1310.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.