QU-GENE: a simulation platform for quantitative analysis of genetic models
QU-GENE: a simulation platform for quantitative analysis of genetic models
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DOI：
10.1093/bioinformatics/14.7.632
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发表时间：
1998-01-01
期刊：
影响因子：
5.8
通讯作者：
Cooper, M
中科院分区：
文献类型：
--
作者：
Podlich, DW;Cooper, M
动机：经典的数量遗传学理论做了许多简化的假设，以发展数学表达式来描述群体内部和群体之间的平均值和变异（遗传和表型），并预测这些在外部环境影响下的预期变化。这些假设通常是必要的，以使理论的许多方面的发展在数学上易于处理。今天高速计算机的可用性为使用计算机模拟方法来研究放宽许多通常做出的假设的影响提供了机会。结果：q - gene （quantitative - genetics）是一个灵活的计算机模拟平台，用于遗传模型的定量分析。q - gene软件的三个特点有助于其灵活性：(i) cole E（N:K）遗传模型，其中E为环境类型的数量，N为基因的数量，K表示上位水平，括号表示不同的N:K遗传模型可以嵌套在不同的环境类型中；（ii）将遗传模型和基因型-环境系统的定义从个体模拟实验的细节中分离出来的两阶段架构的兴起；（iii）使用一系列交互式图形窗口来监控模拟实验的进展。E（N:K）框架能够生成包含基因型-环境（gx E）相互作用和上位性影响的遗传模型家族。通过设计适当的应用模块，可以对任意基因型-环境系统进行多种不同的模拟实验。通过两个实例对q - gene仿真软件的结构进行了说明和论证。第一部分研究了gx E互作对植物育种选择响应的影响，第二部分研究了多峰上位性对四基因上位性网络进化的影响。可获得性：BU-GENE可通过互联网获得：{http://pig.ag.uq.edu.au/qu-gene/}联系：m.cooper @mailbox.uq.edu.au。
Motivation: Classical quantitative genetics theory makes a number of simplifying assumptions in order to develop mathematical expressions that describe the mean and variation (genetic and phenotypic) within and among populations, and to pl edict how these are expected to change under the influence of external for ces. These assumptions ale often necessary to I render the development of many aspects of the theory mathematically tractable. The availability of high-speed computers today provides opportunity for the use of computer simulation methodology to investigate the implications of relaxing many of the assumptions that ale commonly made.Results: QU-GENE (QUantitative-GENEtics) was developed as a flexible computer simulation platform for the quantitative analysis of genetic models. Three features of the QU-GENE software that contribute to its flexibility ale (i) the col-e E(N:K) genetic model, where E is the number of types of environment, N is the number of genes, K indicates the level of epistasis and the parentheses indicate that different ent N:K genetic models can be nested within types of environments, (ii) the rise of a two-stage architecture that separates the definition of the genetic model and genotype-environment system fi om the detail of the individual simulation experiments and (iii) the use of a series of interactive graphical windows that monitor the progress of the simulation experiments. The E(N:K) framework enables the generation of families of genetic models that incorporate the effects of genotype-by-environment (G x E) interactions and epistasis. By the design of appropriate application modules, many different ent simulation experiments can be conducted for any genotype-environment system. The structure e of the QU-GENE simulation software is explained and demonstrated by way of two examples. The first concentrates on some aspects of the influence of G x E interactions on response to selection in plant breeding, and the second considers the influence of multiple-peak epistasis on the evolution of a four-gene epistatic network .Availability: BU-GENE is available over the Internet at {http://pig.ag.uq.edu.au/qu-gene/}Contact: m.cooper @mailbox.uq.edu.au.