Andrew Perry

I have used A Plasmid Editor (ApE) -- http://www.biology.utah.edu/jo... which is platform independent. If you have the genome annotated in Genbank format, it will generate a graphic with the structures annotated. Here's an example of a plasmid that I made and used ApE to make a graphic out of: http://kamrani.net/kambiz/file... Let me know if you have any questions, I can provide a more detailed set of instructions (kambiz@anthropology.net) - Kambiz Kamrani

Ideally it would take a Genbank format (or similar) file with gene annotations, and produce a nice (publication quality ?) picture. Maybe one of the programs for drawing plasmid maps would be good also for this purpose ... I've never seen one I liked but I'm sure it's out there. I'm also familiar with MitoWheel (http://mitowheel.org/mitowheel...) ... it's pretty but only does the human mitochondria, and has a sequence window obscuring the diagram. We want to display various other mitochondrial genome maps. - Andrew Perry

I see, Andrew. Do give ApE a try. I just updated my previous comment with an example of a plasmid graphic I made using ApE. - Kambiz Kamrani

Being part of the Mitowheel developer team I can connect you with the real guy behind, called Gabor Zsurka. Your problem does not seem to me the toughest coding challenge comparing to what Mitowheel already knows. - Attila Csordas

Kambiz: Yes, I'll check out ApE .. my first comment wasn't actually in response to your initial one, it was just extra info .. you were too quick in responding for me ! Thanks ! - Andrew Perry

Attila: That would be great .. I have intended to email him about it anyway, since I think mitoWheel would have far greater utility if it could do any (or many) mito genomes. Unfortunately I'm actually asking for a student in the lab who needs a solution rather ..err.. quickly, so I figured Gabor wouldn't be able to meet her deadline :) In the long term, however, an updated mitoWheel would be excellent. - Andrew Perry

I actually remember trying ApE years ago now ... it's really improved, and I'll probably use it to assist my cloning in the future. Unfortunately, there are too many features (ie ORFs) on many mitochondrial genomes to display everything neatly with ApE ... I need to be able to enlarge the circle, and only display the short gene names (Genbank /gene, not /product) written around the circle, basically the way mitoWheel does it. It might fit if we hand edit the features and tweak the ApE source a little ... - Andrew Perry

Circos makes some nice-looking stuff: http://mkweb.bcgsc.ca/circos/ - Chris Miller