Hi all,
I am a rookie in computational biology and am learning on using python to do some analysis. Could any one give me some advise in the following questions? Thanks a lot!!
In bacteria genome, the 200-300bp before coding sequence (CDS) are usually the regulatory region. There are about 5000 annotated CDS in a certain bacteria strain and I would like to output all the 5000 regulatory regions for the CDS. Is there a package or developed scripts to do so?
Thanks a lot!
Best,
Grace
bedtools flank
bedtools getfasta
Those are the basic steps, assuming you don't have splicing (if you do then you'll need to do some filtering).
Thank you very much Devon. I would not do any splicing. Would there be a tool to convert my .gb file to bed format? Thanks!
Thank you very much Devon. I would not do any splicing. Would there be a tool to convert my .gb file to bed format? Thanks!
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