How to plot gene cluster

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5.2 years ago

sunyeping ▴ 110

Dear all,

I have a fasta sequences of a bacterium operon and I know the gene annotations in it. How should I visualize the gene cluster orgnization like the image in the following link ?

https://drive.google.com/open?id=1s3b0StaKNRTzPQXAkeAZF8ri1Dp8gU13

Do you know any software that can do this?

I will appreciate anyone who can help.

Best regards.

Yeping Sun

plot gene cluster • 1.7k views

ADD COMMENT • link updated 5.2 years ago by Biostar 20 • written 5.2 years ago by sunyeping ▴ 110

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IGV should do the trick no? Are these sequences next to each other?

If not, you can rely on pyGenomeTracks to plot each sequence next to each other in a nice and automated manner: https://github.com/deeptools/pyGenomeTracks

Otherwise, you can use illustrator or Inkscape if you want to just do it for a bunch of sequences, take care to have each feature with a size in mm corresponding to the sequences length so everything is properly scaled.

Another simple way would be to use fancygene, but the tool doesn't exist anymore.

ADD REPLY • link 5.2 years ago by Gautier Richard ▴ 370

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