Question: Gene Cluster/ Synteny Visulization
7
gravatar for Cyatomato
7.5 years ago by
Cyatomato70
Cyatomato70 wrote:

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 • 7.6k views
ADD COMMENTlink modified 7.5 years ago by Bawee10 • written 7.5 years ago by Cyatomato70
3
gravatar for Daniel Standage
7.5 years ago by
Daniel Standage3.9k
Davis, California, USA
Daniel Standage3.9k wrote:

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.

ADD COMMENTlink written 7.5 years ago by Daniel Standage3.9k
2
gravatar for SES
7.5 years ago by
SES8.2k
Vancouver, BC
SES8.2k wrote:

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.

ADD COMMENTlink written 7.5 years ago by SES8.2k
1
gravatar for Bawee
7.5 years ago by
Bawee10
Bawee10 wrote:

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/

ADD COMMENTlink written 7.5 years ago by Bawee10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 791 users visited in the last hour