Upload a File to Draw the Circular Map for Quick Check

Total length of the genome sequence in bp -
Species Name -
Input Format -
Output Image Format -
The input file should be in GFF3 or the simple Tab-delimited format. Sample files can be found here (GFF3, Tab-delimited). -


--The map will show at the end of the page. It may take up to a minute to create the map. The map might display differently for different browser configuration. Please right click the map and then select "Save Image As..." to save the image. Commonly used image processing tools can then be used to adjust the map to the required size and resolution.

--The predicted genes are colored based on their functional group. The color scheme is shown on the left-top of the image. cpgavas support users use of colors in the panel below to label various gene family or genes. In short, open the tab delimited file in your favorite editor and replace the sixth field with the color id in the panel, as indicated by the arrow in the figure below. The required columns in the tab-delimited files are: feature name (column 1), feature type (column 2, should be "rRNA", "tRNA", "mRNA", "Others"), feature start (column 3), feature end (column 4), strand (column 5), color key (column 6, should be "rrn", "trn", protein families such as "rbc", "atp", "psb" and etc, others).

workflow for cpgavas

--There are several excellent web-based tools for drawing chloroplast genome map. These include OrganellarGenomeDRAW, GenomeVX, CGView and etc. We decide not to reinvent the wheel. The drawmap tool is provided to quickly check the correctness of the annotations. For other needs, the users can use the files generated from cpgavas AnnoGenome Module in the generic tab delimited format or GenBank format to create publication-grade maps with tools described above.

--If the image looks strange, (e.g. no genes were drawn or one long gene covers the entire chromosome and etc), please check (1) if you have selected the correct input format. The GFF is the default format. Please select the "Tab_delimited" format if you use the column format as input, and (2) if you have entered the correct length of the genome.


Last updated: July 15th, 2016.
For questions and comments, please send email to cliu@implad.ac.cn or cliu6688@yahoo.com.

Center for Bioinformatics
Institute of Medicinal Plant Development
PeKing Union Medical College
Chinese Academy of Medical Sciences
Address: No. 151, Malianwa North Road, Haidian District, Beijing 100093, P.R.China