GenomeTools

I need to export gene coordinates and exon organisation as a figure. I have prepared the annotations in UniPro Ugene, which I have installed from SBo. A nice tool for graphical representation of such data is provided by the GenomeTools software. It can be easily installed from SBo, too.

So, what is the strategy?

First, in UniPro Ugene select the annotations you want to export, right click and go Export > Export annotations. Then, select the gff format for the exported file, e.g. example.gff.

Now, it’s time to convert example.gff to graphics with the help of GenomeTools. Open up a terminal, navigate to the folder where the example.gff file is and execute the following command:

gt sketch -format svg -style my.style -start 1 -end 40000 output1.svg example.gff

Detailed explanations and instructions can be found in the corresponding section of the GenomeTools web-site.  Brief explanation below:

• gt sketch will use the AnnotationsSketch library to create a drawing
• -format svg specifies the drawing to be a SVG. Other formats include PNG, PDF or PostScript
• -style my.style tells the program to use a custom style file
• -start 1 -end 40000 tells the program to render a sketch between nucleotides 1..40000
• output1.svg is the name of the output file
• example.gff is the name of the input, annotations file

Therefore, this will create a SVG output file from example.gff, called output1.svg, using a custom style for the region between nucleotides 1..40000.

The SVG file can be additionally edited with Inkscape, if necessary. And here’s an example of what GenomeTools can do (from the program’s site):

Beautiful, isn’t it?