GenomeToolsPosted: 2014-09-17 Filed under: academic, drawing, slackbuilds | Tags: gene, genome, genometools, graphics, gt, inkscape, ugene, unipro Leave a comment
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.
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 sketchwill use the AnnotationsSketch library to create a drawing
-format svgspecifies the drawing to be a SVG. Other formats include PNG, PDF or PostScript
-style my.styletells the program to use a custom style file
-start 1 -end 40000tells the program to render a sketch between nucleotides
output1.svgis the name of the output file
example.gffis the name of the input, annotations file
Therefore, this will create a SVG output file from
output1.svg, using a custom style for the region between nucleotides
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?