Department of Biomedical Engineering, One Shields Ave, University of California, Davis, CA 95616, USA.
BMC Bioinformatics. 2013 Jan 16;14:18. doi: 10.1186/1471-2105-14-18.
Cross-species comparisons of gene neighborhoods (also called genomic contexts) in microbes may provide insight into determining functionally related or co-regulated sets of genes, suggest annotations of previously un-annotated genes, and help to identify horizontal gene transfer events across microbial species. Existing tools to investigate genomic contexts, however, lack features for dynamically comparing and exploring genomic regions from multiple species. As DNA sequencing technologies improve and the number of whole sequenced microbial genomes increases, a user-friendly genome context comparison platform designed for use by a broad range of users promises to satisfy a growing need in the biological community.
Here we present JContextExplorer: a tool that organizes genomic contexts into branching diagrams. We implement several alternative context-comparison and tree rendering algorithms, and allow for easy transitioning between different clustering algorithms. To facilitate genomic context analysis, our tool implements GUI features, such as text search filtering, point-and-click interrogation of individual contexts, and genomic visualization via a multi-genome browser. We demonstrate a use case of our tool by attempting to resolve annotation ambiguities between two highly homologous yet functionally distinct genes in a set of 22 alpha and gamma proteobacteria.
JContextExplorer should enable a broad range of users to analyze and explore genomic contexts. The program has been tested on Windows, Mac, and Linux operating systems, and is implemented both as an executable JAR file and java WebStart. Program executables, source code, and documentation is available at http://www.bme.ucdavis.edu/facciotti/resources_data/software/.
在微生物中进行跨物种的基因邻域（也称为基因组上下文）比较，可以深入了解确定功能相关或共同调节的基因集，提示以前未注释基因的注释，并有助于识别跨微生物物种的水平基因转移事件。然而，现有的用于研究基因组上下文的工具缺乏动态比较和探索多个物种基因组区域的功能。随着 DNA 测序技术的改进和整个微生物基因组测序数量的增加，一个为广大用户设计的用户友好的基因组上下文比较平台有望满足生物界日益增长的需求。
我们在此提出 JContextExplorer：一种将基因组上下文组织成分支图的工具。我们实现了几种替代的上下文比较和树渲染算法，并允许轻松在不同的聚类算法之间进行转换。为了促进基因组上下文分析，我们的工具实现了 GUI 功能，例如文本搜索过滤、单个上下文的点击查询以及通过多基因组浏览器进行基因组可视化。我们通过尝试解决一组 22 个α和γ变形菌中两个高度同源但功能不同的基因之间的注释歧义来展示我们工具的一个用例。
JContextExplorer 应该能够使广泛的用户能够分析和探索基因组上下文。该程序已在 Windows、Mac 和 Linux 操作系统上进行了测试，并且既作为可执行 JAR 文件又作为 Java WebStart 实现。程序可执行文件、源代码和文档可在 http://www.bme.ucdavis.edu/facciotti/resources_data/software/ 获得。
