Fast and flexible simulation of DNA sequence data

被引：273

作者：

Chen, Gary K. ^{[1
,2
,3
]}

Marjoram, Paul ^{[2
]}

Wall, Jeffrey D. ^{[1
,3
]}

机构：

[1] Univ Calif San Francisco, Inst Human Genet, San Francisco, CA 94143 USA

[2] Univ Calif Los Angeles, Dept Prevent Med, Los Angeles, CA 90033 USA

[3] Univ Calif San Francisco, Dept Epidemiol & Biostat, San Francisco, CA 94143 USA

来源：

GENOME RESEARCH | 2009年 / 19卷 / 01期

基金：

美国国家卫生研究院;

关键词：

LINKAGE DISEQUILIBRIUM; GENE CONVERSION; COALESCENT SIMULATION; HUMAN GENOME; RECOMBINATION; POPULATION; POLYMORPHISM; MODELS; DIVERSITY; SELECTION;

D O I：

10.1101/gr.083634.108

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Simulation of genomic sequences under the coalescent with recombination has conventionally been impractical for regions beyond tens of megabases. This work presents an algorithm, implemented as the program MaCS (Markovian Coalescent Simulator), that can efficiently simulate haplotypes under any arbitrary model of population history. We present several metrics comparing the performance of MaCS with other available simulation programs. Practical usage of MaCS is demonstrated through a comparison of measures of linkage disequilibrium between generated program output and real genotype data from populations considered to be structured.

引用

页码：136 / 142

页数：7

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