Grasp the 200bp gene sequence before all coding sequence in a bacteria genome

Question

[gaoyanwang]

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

Answer 1

[Devon Ryan]

 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).

[gaoyanwang]

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!

Answer 2

[gaoyanwang]

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!