Haplotyping Problem, A Clustering Approach
Journal Article
·
· AIP Conference Proceedings
- Faculty of Mathematics, Shahid-Beheshti University, Tehran (Iran, Islamic Republic of)
- National Institute for Genetic Engineering and Biotechnology, Tehran-Karaj Highway, Tehran (Iran, Islamic Republic of)
- Center of Excellence in Biomathematics, School of Mathematics, Statistics and Computer Science, University College of Science, University of Tehran, Tehran (Iran, Islamic Republic of)
- Department of Computer Engineering, Sharif University of Technology, Tehran (Iran, Islamic Republic of)
Construction of two haplotypes from a set of Single Nucleotide Polymorphism (SNP) fragments is called haplotype reconstruction problem. One of the most popular computational model for this problem is Minimum Error Correction (MEC). Since MEC is an NP-hard problem, here we propose a novel heuristic algorithm based on clustering analysis in data mining for haplotype reconstruction problem. Based on hamming distance and similarity between two fragments, our iterative algorithm produces two clusters of fragments; then, in each iteration, the algorithm assigns a fragment to one of the clusters. Our results suggest that the algorithm has less reconstruction error rate in comparison with other algorithms.
- OSTI ID:
- 21035858
- Journal Information:
- AIP Conference Proceedings, Vol. 936, Issue 1; Conference: International conference on numerical analysis and applied mathematics, Corfu (Greece), 16-20 Sep 2007; Other Information: DOI: 10.1063/1.2790104; (c) 2007 American Institute of Physics; Country of input: International Atomic Energy Agency (IAEA); ISSN 0094-243X
- Country of Publication:
- United States
- Language:
- English
Similar Records
Haplotypes in the APOA1-C3-A4-A5 gene cluster affect plasma lipids in both humans and baboons
The association of XRCC1 haplotypes and chromosomal damage levels in peripheral blood lymphocyte among coke-oven workers
A Novel Coarsening Method for Scalable and Efficient Mesh Generation
Journal Article
·
Mon Sep 15 00:00:00 EDT 2003
· Human Molecular Genetics
·
OSTI ID:21035858
+7 more
The association of XRCC1 haplotypes and chromosomal damage levels in peripheral blood lymphocyte among coke-oven workers
Journal Article
·
Sun May 15 00:00:00 EDT 2005
· Cancer Epidemiology, Biomarkers and Prevention
·
OSTI ID:21035858
+6 more
A Novel Coarsening Method for Scalable and Efficient Mesh Generation
Technical Report
·
Thu Dec 02 00:00:00 EST 2010
·
OSTI ID:21035858