CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes.
CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes.
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DOI：
10.1186/1471-2105-7-472
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发表时间：
2006-10-24
影响因子：
3
通讯作者：
Kobayashi I
中科院分区：
文献类型：
--
作者：
Uchiyama I;Higuchi T;Kobayashi I
最近积累的密切相关的基因组序列提供了一个宝贵的资源，阐明各种生物的进化历史。然而，尽管迄今为止已经开发了许多比对计算和可视化工具，但复杂基因组变化（例如大的插入、缺失、倒位、易位和重复）的分析仍然存在一定的困难。我们已经开发了一个比较基因组分析工具，名为CGAT，它允许密切相关的细菌大小的基因组的详细比较，主要是通过可视化中到大规模的变化，以推断潜在的机制。CGAT在点图和比对查看器上显示预先计算的成对基因组比对，具有滚动和缩放功能，并允许用户沿着预先确定的正向比对移动。用户可以将几种类型的信息放在这种比对上，例如串联重复序列或散布的重复序列的存在以及G+C含量或密码子使用偏好的变化，从而促进对观察到的基因组变化的解释。除了显示预先计算的对齐之外，查看器还可以动态计算指定区域之间的对齐;此功能对于检查对齐边界特别有用，因为这些边界通常是模糊的，并且在程序之间可能会有所不同。除了比对浏览器功能外，CGAT还包含比对数据构建模块，该模块包含通常用于大规模比对计算的预处理和后处理的各种程序，例如用于计算长比对、链接相邻比对和直系同源物识别的拆分和合并协议。事实上，CGAT提供了一个通用框架，用于使用各种现有程序作为比对引擎计算基因组规模的比对，这允许用户比较不同比对程序的输出。该程序的早期版本已成功地用于我们的研究，以推断密切相关的真细菌和古细菌之间明显复杂的基因组变化的进化历史。CGAT是一种实用的工具，用于使用现有的比对程序和其他序列分析工具结合广泛的手动检查来分析密切相关的基因组之间的复杂基因组变化。
The recent accumulation of closely related genomic sequences provides a valuable resource for the elucidation of the evolutionary histories of various organisms. However, although numerous alignment calculation and visualization tools have been developed to date, the analysis of complex genomic changes, such as large insertions, deletions, inversions, translocations and duplications, still presents certain difficulties. We have developed a comparative genome analysis tool, named CGAT, which allows detailed comparisons of closely related bacteria-sized genomes mainly through visualizing middle-to-large-scale changes to infer underlying mechanisms. CGAT displays precomputed pairwise genome alignments on both dotplot and alignment viewers with scrolling and zooming functions, and allows users to move along the pre-identified orthologous alignments. Users can place several types of information on this alignment, such as the presence of tandem repeats or interspersed repetitive sequences and changes in G+C contents or codon usage bias, thereby facilitating the interpretation of the observed genomic changes. In addition to displaying precomputed alignments, the viewer can dynamically calculate the alignments between specified regions; this feature is especially useful for examining the alignment boundaries, as these boundaries are often obscure and can vary between programs. Besides the alignment browser functionalities, CGAT also contains an alignment data construction module, which contains various procedures that are commonly used for pre- and post-processing for large-scale alignment calculation, such as the split-and-merge protocol for calculating long alignments, chaining adjacent alignments, and ortholog identification. Indeed, CGAT provides a general framework for the calculation of genome-scale alignments using various existing programs as alignment engines, which allows users to compare the outputs of different alignment programs. Earlier versions of this program have been used successfully in our research to infer the evolutionary history of apparently complex genome changes between closely related eubacteria and archaea. CGAT is a practical tool for analyzing complex genomic changes between closely related genomes using existing alignment programs and other sequence analysis tools combined with extensive manual inspection.
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影响因子：
14.9
作者：
Ishikawa, Ken;Watanabe, Miki;Kuroita, Toshihiro;Uchiyama, Ikuo;Bujnicki, Janusz M;Kawakami, Bunsei;Tanokura, Masaru;Kobayashi, Ichizo
通讯作者：
Kobayashi, Ichizo
影响因子：
14.9
作者：
GILSON, E;SAURIN, W;HOFNUNG, M
通讯作者：
HOFNUNG, M
影响因子：
3.5
作者：
Chinen, A;Uchiyama, I;Kobayashi, I
通讯作者：
Kobayashi, I
影响因子：
7
作者：
Jareborg, N;Durbin, R
通讯作者：
Durbin, R
影响因子：
64.8
作者：
Alm, RA;Ling, LSL;Trost, TJ
通讯作者：
Trost, TJ