Jayashree B, Rajgopal S, Hoisington D, Prasanth V P, Chandra S
Bioinformatics Unit, ICRISAT, Patancheru 502324, Andhra Pradeesh, India.
J Integr Bioinform. 2008 Sep 24;5(1):89. doi: 10.2390/biecoll-jib-2008-89.
Structure, is a widely used software tool to investigate population genetic structure with multi-locus genotyping data. The software uses an iterative algorithm to group individuals into "K" clusters, representing possibly K genetically distinct subpopulations. The serial implementation of this programme is processor-intensive even with small datasets. We describe an implementation of the program within a parallel framework. Speedup was achieved by running different replicates and values of K on each node of the cluster. A web-based user-oriented GUI has been implemented in PHP, through which the user can specify input parameters for the programme. The number of processors to be used can be specified in the background command. A web-based visualization tool "Visualstruct", written in PHP (HTML and Java script embedded), allows for the graphical display of population clusters output from Structure, where each individual may be visualized as a line segment with K colors defining its possible genomic composition with respect to the K genetic sub-populations. The advantage over available programs is in the increased number of individuals that can be visualized. The analyses of real datasets indicate a speedup of up to four, when comparing the speed of execution on clusters of eight processors with the speed of execution on one desktop. The software package is freely available to interested users upon request.
Structure是一个广泛使用的软件工具，用于利用多位点基因分型数据研究群体遗传结构。该软件使用迭代算法将个体分组为“K”个簇，代表可能的K个遗传上不同的亚群。即使是小数据集，该程序的串行实现也需要大量处理器资源。我们描述了该程序在并行框架中的一种实现方式。通过在集群的每个节点上运行不同的重复样本和K值来实现加速。基于网络的面向用户的图形用户界面（GUI）已用PHP实现，用户可以通过它为程序指定输入参数。要使用的处理器数量可以在后台命令中指定。基于网络的可视化工具“Visualstruct”用PHP编写（嵌入了HTML和JavaScript），可以对Structure输出的群体簇进行图形显示，其中每个个体可以可视化为一条线段，用K种颜色定义其相对于K个遗传亚群的可能基因组组成。与现有程序相比，其优势在于可以可视化的个体数量增加。对真实数据集的分析表明，将八个处理器的集群上的执行速度与一台台式机上的执行速度进行比较时，加速比高达四倍。感兴趣的用户可通过请求免费获得该软件包。
