Programs for drawing a circular mitochondrial map, Circos or others?

Question

[Yongjie Zhang]

Dear All,

I want to draw a circular map for a mitochondrial genome. Could you please suggest programs that you know is powerful to do so? I want genes in the mitogenome to be marked by text and color blocks.

I know Circos can be used to draw a circular map but not sure if it can have different gene blocks marked by different colors. Examples/tutorial provided by Circos are all for different chromosomes, each of which can have a different color. What should I do in order to show different genes in the chromosome (i.e., my mitogenome) with different colors?

Thanks for any comments.

Yongjie

[5heikki]

1. Circos does have a recipe for a single chromosome

2. There are many threads about circular genome visualization, e.g. here and here (use the search)

Answer 1

[wl284]

This program OrganellarGenomeDRAW might be useful http://ogdraw.mpimp-golm.mpg.de/

OrganellarGenomeDRAW (OGDRAW) - a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Lohse, M., Drechsel, O. and Bock, R.. Curr. Genet. (2007) 52:267-274.

Answer 2

[Joe]

Circos, Anvio and BRIG should all do what you want.

I've never used circos but have used the other 2 if you need more info. BRIG was developed by a guy in my lab.

Answer 3

[s.j.goodman]

There's a new (July 2024) standalone application (circularMT) for Windows/Mac/Linux for drawing publication quality mitochondrial genome diagrams. Runs with a GUI or from the command line. Generates circular and linear maps with a high level of user defined customisation.

https://academic.oup.com/bioinformatics/article/40/7/btae450/7713370

[GenoMax]

s.j.goodman : Looks like you are the developer of this tool. It would be best to create a new post using tool classification. Provide information about the program e.g. where people can download, quick-guide on how to use etc. Look at some of the past tools posts to get an idea.