Haplotype reconstruction from SNP fragments by minimum error correction
نویسندگان
چکیده
منابع مشابه
Haplotype reconstruction from SNP fragments by minimum error correction
MOTIVATION Haplotype reconstruction based on aligned single nucleotide polymorphism (SNP) fragments is to infer a pair of haplotypes from localized polymorphism data gathered through short genome fragment assembly. An important computational model of this problem is the minimum error correction (MEC) model, which has been mentioned in several literatures. The model retrieves a pair of haplotype...
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Single Nucleotide Polymorphisms (SNPs), a single DNA base varying from one individual to another, are believed to be the most frequent form responsible for genetic differences. Haplotypes have more information for disease-associating than individual SNPs or genotypes; it is substantially more difficult to determine haplotypes through experiments. Hence, computational methods that can reduce the...
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Given an assembled genome of a diploid organism the haplotype assembly problem can be formulated as retrieval of a pair of haplotypes from a set of aligned weighted SNP fragments. Known computational formulations (models) of this problem are minimum letter flips (MLF) and the weighted minimum letter flips (WMLF; Greenberg et al. (INFORMS J. Comput. 2004, 14, 211-213)). In this paper we show tha...
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In this paper, we develop a probabilistic model to approach two realistic scenarios regarding the singular haplotype reconstruction problem--the incompleteness and inconsistency that occurred in the DNA sequencing process to generate the input haplotype fragments, and the common practice used to generate synthetic data in experimental algorithm studies. We design three algorithms in the model t...
متن کاملEnhanced Evolutionary and Heuristic Algorithms for Haplotype Reconstruction Problem Using Minimum Error Correction Model
Construction of two haplotypes from a set of Single Nucleotide Polymorphism (SNP) fragments is referred to as haplotype reconstruction problem. One of the most important computational models for this problem is Minimum Error Correction (MEC). Since MEC is an NP-hard problem, here we propose a heuristic algorithm for haplotype reconstruction problem. The algorithm is Particle Swarm Optimization ...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2005
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/bti352