Gene Cluster/ Synteny Visulization
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9.6 years ago
Cyatomato ▴ 70

alt text

I need to draw some graphs like above to show the conserved gene order between different strains. So do you know some software can draw such a graph automaticly. Because I have a long list to draw. And I have the genbank/ptt/gff format file, I hope that software can read one of those format.

Thank you very much!

gene visualization • 9.0k views
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3
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9.6 years ago

The AnnotationSketch tool (part of the GenomeTools library) can read data in GFF3 format and generate PNG graphics. Color coding is highly configurable, but I the legend wouldn't be possible without some post-processing with something like Photoshop or Gimp.

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9.6 years ago
SES 8.5k

Since you have gff files already, I would recommend GBrowse_syn, though I have to warn that if you are not familiar with GBrowse already then configuring GBrowse_syn may not be worth the effort just to create some graphs (you need a database of alignments, not just annotations, for this to work). SynView is another synteny viewer that uses GBrowse, but with a completely different design. SynView ships with some test data and I know the author still works on related projects, so he will likely be helpful. If you are starting from scratch, you could just use Mauve, which will create a graph showing the synteny between the genomes.

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9.6 years ago
Bawee ▴ 10

Try this. It has a friendly user interface and is very easy to use. Scaleable to a large number of genomes. Also does labels. http://sourceforge.net/projects/easyfig/

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