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Haplotyping problem, a clustering approach

Eslahchi, C ; Sharif University of Technology | 2007

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  1. Type of Document: Article
  2. DOI: 10.1063/1.2790104
  3. Publisher: 2007
  4. Abstract:
  5. 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. © 2007 American Institute of Physics
  6. Keywords:
  7. Clustering analysis ; Haplotype reconstruction ; MEC model ; SNP fragment
  8. Source: NUMERICAL ANALYSIS AND APPLIED MATHEMATICS: International Conference on Numerical Analysis and Applied Mathematics, Corfu, 16 September 2007 through 20 September 2007 ; Volume 936 , 2007 , Pages 185-190 ; 0094243X (ISSN) ; 073540447X (ISBN); 9780735404472 (ISBN)
  9. URL: https://aip.scitation.org/doi/abs/10.1063/1.2790104