Alfresco - A workbench for comparative genomic sequence analysis
Alfresco - A workbench for comparative genomic sequence analysis
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DOI：
10.1101/gr.10.8.1148
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发表时间：
2000-08-01
期刊：
影响因子：
7
通讯作者：
Durbin, R
中科院分区：
文献类型：
--
作者：
Jareborg, N;Durbin, R
基因组序列的比较分析为确定潜在的生物功能区域提供了强有力的工具；通过比较来自合适物种的基因组的相应区域，可以根据它们的同源性来识别蛋白质编码或调节区。这需要使用几种特定类型的计算分析工具。对于这些类型的分析，存在许多程序；用于全面查看/控制结果的程序不多，这是大规模基因组序列分析所必需的。使用熔岩，我们开发了一种新的可视化工具，可以进行有效的比较基因组序列分析。该程序处理一对来自不同物种推定同源区域的序列。来自各种不同的现有外部分析程序(例如数据库搜索、基因预测、重复屏蔽和比对程序)的结果被可视化，并用于在两个序列中寻找对应的功能序列结构域。用户通过基因组区域的图形显示与程序交互，其中显示了序列的独立可滚动和可缩放的符号表示。作为一个例子，分析了来自人类和小鼠的两个未注释的同源基因组序列，其中包含部分UTY基因座。
Comparative analysis of genomic sequences provides a powerful tool For identifying regions of potential biologic function; by comparing corresponding regions of genomes from suitable species, protein coding or regulatory regions can be identified by their homology. This requires the use of several specific types of computational analysis tools. Many programs exist for these types of analysis; not many exist for overall view/control of the results, which is necessary For large-scale genomic sequence analysis. Using lava, we have developed a new visualization tool that allows Effective comparative genome sequence analysis. The program handles a pair of sequences from putatively homologous regions in different species. Results from various different existing external analysis programs, such as database searching, gene prediction, repeat masking, and alignment programs, are visualized and used to find corresponding Functional sequence domains in the two sequences. The user interacts with the program through a graphic display of the genome regions, in which an independently scrollable and zoomable symbolic representation of the sequences is shown. As an example, the analysis of two unannotated orthologous genomic sequences from human and mouse containing parts of the UTY locus is presented.