Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA.
Methods Mol Biol. 2023;2545:19-45. doi: 10.1007/978-1-0716-2561-3_2.
The CoGe software suite at genomevolution.org hosts a number of tools that facilitate genomic research on plant and animal whole-genome multiplication-polyploidy. SynMap permits analysis and visualization of two-way syntenic dotplot alignments of genomes, includes many options and data/graphics download possibilities, and even permits three-genome synteny maps and interactive views. FractBias is a tool that operates within SynMap that permits calculation and graphic display of genome fragments (such as chromosomes) of one species mapped to another, displaying both blockwise homology depths and the extent of syntenic gene (syntelog) loss following polyploidy events. SynMap macrosynteny results can segue into the microsynteny tool GEvo, which provides genome-browser-like views of homologous genome blocks. CoGe FeatView allows call-up of given gene features already stored in the CoGe resource, and CoGeBlast permits searches for additional features that can be analyzed or downloaded further. Links from these tools can be fed into SynFind, which can find syntenic blocks surrounding a feature across multiple specified genomes while also simultaneously providing overall genome-wide syntenic depth calculations that can be interpreted to reflect polyploidy levels. Here, we describe basic use of these tools on the CoGe software suite.
genomevolution.org 上的 CoGe 软件套件提供了许多工具，可方便对植物和动物全基因组倍增-多倍体的基因组研究。SynMap 允许对基因组的双向同线性点图比对进行分析和可视化，包括许多选项和数据/图形下载功能，甚至允许三基因组同线性图谱和交互式视图。FractBias 是 SynMap 内的一个工具，允许计算和图形显示映射到另一个物种的一个物种的基因组片段（如染色体），显示同源深度的块状和多倍体事件后同线性基因（syntelog）丢失的程度。SynMap 宏同线性结果可以进入微同线性工具 Gevo，它提供类似基因组浏览器的同源基因组块视图。CoGe FeatView 允许调用已经存储在 CoGe 资源中的给定基因特征，而 CoGeBlast 允许搜索其他可以分析或进一步下载的特征。这些工具的链接可以输入到 SynFind 中，SynFind 可以在多个指定的基因组中找到围绕特征的同线性块，同时还提供整体全基因组同线性深度计算，可用于反映多倍体水平。在这里，我们描述了这些工具在 CoGe 软件套件上的基本用法。
