Grant Jason R, Stothard Paul
Department of Agricultural, Food and Nutritional Science, University of Alberta, Canada.
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W181-4. doi: 10.1093/nar/gkn179. Epub 2008 Apr 14.
The CGView Server generates graphical maps of circular genomes that show sequence features, base composition plots, analysis results and sequence similarity plots. Sequences can be supplied in raw, FASTA, GenBank or EMBL format. Additional feature or analysis information can be submitted in the form of GFF (General Feature Format) files. The server uses BLAST to compare the primary sequence to up to three comparison genomes or sequence sets. The BLAST results and feature information are converted to a graphical map showing the entire sequence, or an expanded and more detailed view of a region of interest. Several options are included to control which types of features are displayed and how the features are drawn. The CGView Server can be used to visualize features associated with any bacterial, plasmid, chloroplast or mitochondrial genome, and can aid in the identification of conserved genome segments, instances of horizontal gene transfer, and differences in gene copy number. Because a collection of sequences can be used in place of a comparison genome, maps can also be used to visualize regions of a known genome covered by newly obtained sequence reads. The CGView Server can be accessed at http://stothard.afns.ualberta.ca/cgview_server/
CGView服务器生成环状基因组的图形图谱，展示序列特征、碱基组成图、分析结果和序列相似性图。序列可以以原始格式、FASTA格式、GenBank格式或EMBL格式提供。额外的特征或分析信息可以以GFF（通用特征格式）文件的形式提交。该服务器使用BLAST将主序列与多达三个比较基因组或序列集进行比较。BLAST结果和特征信息被转换为一个展示整个序列的图形图谱，或者一个感兴趣区域的扩展且更详细的视图。包含了几个选项来控制显示哪些类型的特征以及如何绘制这些特征。CGView服务器可用于可视化与任何细菌、质粒、叶绿体或线粒体基因组相关的特征，并有助于识别保守的基因组片段、水平基因转移的实例以及基因拷贝数的差异。由于可以使用一组序列来代替比较基因组，图谱也可用于可视化新获得的序列读数所覆盖的已知基因组区域。可通过http://stothard.afns.ualberta.ca/cgview_server/访问CGView服务器。
