کد مقاله | کد نشریه | سال انتشار | مقاله انگلیسی | نسخه تمام متن |
---|---|---|---|---|
1141058 | 956760 | 2009 | 12 صفحه PDF | دانلود رایگان |
عنوان انگلیسی مقاله ISI
Self-organizing map approaches for the haplotype assembly problem
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کلمات کلیدی
موضوعات مرتبط
مهندسی و علوم پایه
سایر رشته های مهندسی
کنترل و سیستم های مهندسی
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چکیده انگلیسی
Haplotype assembly is to reconstruct a pair of haplotypes from SNP values observed in a set of individual DNA fragments. In this paper, we focus on studying minimum error correction (MEC) model for the haplotype assembly problem and explore self-organizing map (SOM) methods for this problem. Specifically, haplotype assembly by MEC is formulated into an integer linear programming model. Since the MEC problem is NP-hard and thus cannot be solved exactly within acceptable running time for large-scale instances, we investigate the ability of classical SOMs to solve the haplotype assembly problem with MEC model. Then, aiming to overcome the limits of classical SOMs, a novel SOM approach is proposed for the problem. Extensive computational experiments on both synthesized and real datasets show that the new SOM-based algorithm can efficiently reconstruct haplotype pairs in a very high accuracy under realistic parameter settings. Comparison with previous methods also confirms the superior performance of the new SOM approach.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Mathematics and Computers in Simulation - Volume 79, Issue 10, June 2009, Pages 3026-3037
Journal: Mathematics and Computers in Simulation - Volume 79, Issue 10, June 2009, Pages 3026-3037
نویسندگان
Ling-Yun Wu, Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen,