Simulation of genomes: a review.

作者: Antonio Carvajal-Rodriguez

DOI: 10.2174/138920208784340759

关键词: TRACE (psycholinguistics)Key (cryptography)Data scienceField (computer science)Empirical researchPopulation geneticsComputer scienceContrast (statistics)Natural selectionEmpirical evidence

摘要: There is an increasing role of population genetics in human genetic research linking empirical observations with hypotheses about sequence variation due to historical and evolutionary causes. In addition, the data sets are size, genome-wide becoming a common place many studies. As far as more information available, it becomes clear that simplest not consistent data. Simulations will provide key tool contrast complex on real by generating simulated under hypothetical conditions we want contrast. Undoubtedly, developing tools for simulating large sequences at same time allow simulate natural selection, recombination demography patterns be great interest order better understanding trace left DNA different interacting forces. Simulation also essential evaluate sampling properties any statistics used association studies compare performance methods applied scales. Several recent simulation have been developed. Here, review some currently existing simulators which efficient scenarios. point out future directions this field already part current biology seems primary genome post-genomic biology.

参考文章(36)
A. R. Rogers, S. Wooding, C. D. Huff, M. A. Batzer, L. B. Jorde, Ancestral Alleles and Population Origins: Inferences Depend on Mutation Rate Molecular Biology and Evolution. ,vol. 24, pp. 990- 997 ,(2007) , 10.1093/MOLBEV/MSM018
Thomas Mailund, Mikkel H Schierup, Christian NS Pedersen, Peter JM Mechlenborg, Jesper N Madsen, Leif Schauser, None, CoaSim: A flexible environment for simulating genetic data under coalescent models BMC Bioinformatics. ,vol. 6, pp. 252- 252 ,(2005) , 10.1186/1471-2105-6-252
Montserrat Aguadé, Humberto Quesada, Sebastián E. Ramos-Onsins, Julio Rozas, Positive Selection Versus Demography: Evolutionary Inferences Based on an Unusual Haplotype Structure in Drosophila simulans Molecular Biology and Evolution. ,vol. 23, pp. 1643- 1647 ,(2006) , 10.1093/MOLBEV/MSL031
Sheng Gu, Andrew J Pakstis, Hui Li, William C Speed, Judith R Kidd, Kenneth K Kidd, Significant variation in haplotype block structure but conservation in tagSNP patterns among global populations. European Journal of Human Genetics. ,vol. 15, pp. 302- 312 ,(2007) , 10.1038/SJ.EJHG.5201751
John Wakeley, The limits of theoretical population genetics. Genetics. ,vol. 169, pp. 1- 7 ,(2005) , 10.1093/GENETICS/169.1.1
Clive J. Hoggart, Marc Chadeau-Hyam, Taane G. Clark, Riccardo Lampariello, John C. Whittaker, Maria De Iorio, David J. Balding, Sequence-Level Population Simulations Over Large Genomic Regions Genetics. ,vol. 177, pp. 1725- 1731 ,(2007) , 10.1534/GENETICS.106.069088
M. Currat, N. Ray, L. Excoffier, splatche: a program to simulate genetic diversity taking into account environmental heterogeneity Molecular Ecology Notes. ,vol. 4, pp. 139- 142 ,(2004) , 10.1046/J.1471-8286.2003.00582.X