VIRAPOPS：一种专门用于快速进化病毒群体的正向模拟器。

VIRAPOPS: a forward simulator dedicated to rapidly evolved viral populations.

机构信息

Department of Biology, Univ Paris Diderot, Sorbonne Paris Cité, MTI, INSERM UMR-S 973, CNRS, UMR7592, Institut Jacques Monod, F-75013 Paris and Atelier de Bio Informatique, F-75005 Paris, France.

出版信息

Bioinformatics. 2014 Feb 15;30(4):578-80. doi: 10.1093/bioinformatics/btt724. Epub 2013 Dec 12.

DOI:10.1093/bioinformatics/btt724

PMID:24336644

Abstract

SUMMARY

Daily, mutability and recombination of RNA viruses result in the production of million variants. All these rapid genomic changes directly influence the functional sites of the protein, its 3D structure or its drug resistances. Therefore, it is important to simulate these drastic switches to determine their effects on virus populations. Many computer programs are able to simulate specific variations in DNA genomes, but are generally non-adapted to RNA viruses. They simulate site-specific selection pressures, but rarely pressures on covariant or on higher order correlated sites and no at all on synthetic lethal groups. That is why we felt it important to create VIRAPOPS, a forward simulator that models specific RNA virus functions. It was designed for computational biologists, biologists and virologists.

AVAILABILITY AND IMPLEMENTATION

Free binaries are available through a software repository at http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html.

摘要

每天，RNA 病毒的变异性和重组导致产生上百万种变体。所有这些快速的基因组变化直接影响蛋白质的功能位点、其 3D 结构或其耐药性。因此，模拟这些剧烈变化以确定它们对病毒群体的影响非常重要。许多计算机程序能够模拟 DNA 基因组的特定变异，但通常不适应 RNA 病毒。它们模拟特定位置的选择压力，但很少模拟共变或更高阶相关位置的压力，更不会模拟合成致死群的压力。这就是为什么我们觉得有必要创建 VIRAPOPS，这是一个用于模拟特定 RNA 病毒功能的正向模拟器。它是为计算生物学家、生物学家和病毒学家设计的。