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هفتمین همایش بیو انفورماتیک ایران
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| عنوان فارسی |
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| چکیده فارسی مقاله |
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| کلیدواژه‌های فارسی مقاله |
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| عنوان انگلیسی |
Haplotype Assembly Using Rank Minimization |
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| چکیده انگلیسی مقاله |
For many years, DNA sequencing was done using Sanger’s method introduced in 1975. Nowdays, Next Generation Sequencing (NGS) becomes popular due to its speed and resolution [1]. In diploids, there are two homologous copies of each somatic chromosome. Homologous pairs mean that each chromosome consists of similar nucleotides sequences except a little difference. The frequent variation of a single nucleotide is named as the Single Nucleotide Polymorphism (SNP). The sequence of SNPs of each chromosome is called haplotype. The haplotype of an individual is used in drug-design and genome wide association studies [2]. Unfortunately, NGS does not provide haplotype information. Haplotype can be found using high-cost experiments or computational methods [3]. Using the NGS data for Haplotyping is known as haplotype assembly which is a NP-Hard problem. A new method for haplotype assembly is SDhaP [4] which is superior to ReFHap [2] and HapCut [5]. The core idea of SDhaP is correlation clustering. In this paper, a novel modeling for the haplotype data and NGS reads is presented based on [6]. This model results in a constraint on the rank of the read matrix. Then, the problem of haplotype assembly converted to a rank minimization optimization. Since the rank functional which is from vector space of matrices to the positive integer set, is non-convex, it can be relaxed to the nuclear norm, i.e. the sum of matrix singular values. This relaxation has been well mentioned as the power of convex relaxation [7-8]. Simulations on the data addressed in [9] shows that the proposed approach improves the resolution of haplotype assembly in terms of reconstruction rate compared to the new method, SDhaP [4]. |
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| کلیدواژه‌های انگلیسی مقاله |
Haplotype Assembly, Next Generation Sequencing (NGS), Rank minimization. |
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| نویسندگان مقاله |
S. Majidian - Iran University of Science & Technology, Narmak, Tehran,
M. H. Kahaei - Iran University of Science & Technology, Narmak, Tehran,
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| نشانی اینترنتی |
http://www.icb7.ir |
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| زبان مقاله منتشر شده |
en |
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