【摘要】 Circos软件是一款功能强大的用于基因组比较分析数据可视化的图形生成软件,但是该软件需要使用者自己编程提取所需数据,因此如何将基因组注释和比较分析结果与该软件衔接是个非常实际的问题.这里,我们开发了一个能够将基因组数据快速与Circos^[1]软件衔接的工具一Geno2Cir.这个工具可以处理对位排列好的基因组数据,进行物种间序列差异的比较,得到能够直接用于生成Circos图像的文件.本工具不仅可以进行基因组之间的两两比较,也可以进行多个基因组之间的同时比较.前者利用窗口步移法进行序列之间的直接比较,后者利用K2P（Kimura-2-parameter）方法先计算两两序列之间的距离,然后得到所有序列之间的距离矩阵之后再计算总体的差异.这一工具可以应用于裸子植物松属物种的叶绿体基因组,以及亲缘关系较远但是序列差异较小的凤蝶总科线粒体基因组的比较.更多还原

【Abstract】 Circos is a widely used data visualization tool,but incapable of handling raw sequence data by itself,especially for genomic level data,which requires great effort on programming and data mining.Here,we developed a tool—Geno2Cir to bridge raw genomic data to Circos directly.This tool is able to deal with aligned genomic sequences,compare the extent of differences between different species,and to generate files that can be visualized by Circos directly.This tool not only deals with pair-wise comparison of genomes,but also multiple comparison of genomes.The former one is realized by window-walking method to compare two sequences directly in a certain size of window and pace length.The latter one is realized by calculating pair-wise Kimura 2-parameter distance,then the overall difference by distance matrix.This tool was used in chloroplast genomes of gymnosperm species,Pinus,and mitochondrial genomes of Papilionoidea species,which are distantly related species.We found common and different evolution history footprints.更多还原