Max Planck Institute for Developmental Biology, Department I, Protein Evolution, Spemannstr. 35, 72076 Tübingen, Germany.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W353-6. doi: 10.1093/nar/gkr364. Epub 2011 May 23.
Genomic neighborhood can provide important insights into evolution and function of a protein or gene. When looking at operons, changes in operon structure and composition can only be revealed by looking at the operon as a whole. To facilitate the analysis of the genomic context of a query in multiple organisms we have developed Genomic Context Viewer (GCView). GCView accepts results from one or multiple protein homology searches such as BLASTp as input. For each hit, the neighboring protein-coding genes are extracted, the regions of homology are labeled for each input and the results are presented as a clear, interactive graphical output. It is also possible to add more searches to iteratively refine the output. GCView groups outputs by the hits for different proteins. This allows for easy comparison of different operon compositions and structures. The tool is embedded in the framework of the Bioinformatics Toolkit of the Max-Planck Institute for Developmental Biology (MPI Toolkit). Job results from the homology search tools inside the MPI Toolkit can be forwarded to GCView and results can be subsequently analyzed by sequence analysis tools. Results are stored online, allowing for later reinspection. GCView is freely available at http://toolkit.tuebingen.mpg.de/gcview.
基因组邻居关系可以为蛋白质或基因的进化和功能提供重要的见解。在研究操纵子时，只有将操纵子作为一个整体来看，才能揭示操纵子结构和组成的变化。为了便于在多个生物体中分析查询的基因组背景，我们开发了基因组上下文查看器 (GCView)。GCView 接受来自 BLASTp 等一种或多种蛋白质同源搜索的结果作为输入。对于每个命中，提取相邻的编码蛋白质的基因，为每个输入标记同源区域，并以清晰的交互图形输出呈现结果。也可以添加更多搜索来迭代地优化输出。GCView 根据不同蛋白质的命中结果对输出进行分组。这允许轻松比较不同操纵子的组成和结构。该工具嵌入在马克斯·普朗克发育生物学研究所 (MPI) 的生物信息学工具包 (MPI 工具包) 中。来自 MPI 工具包中同源搜索工具的作业结果可以转发到 GCView，随后可以使用序列分析工具对结果进行分析。结果在线存储，允许以后重新检查。GCView 可免费在 http://toolkit.tuebingen.mpg.de/gcview 获得。
