Grasp the 200bp gene sequence before all coding sequence in a bacteria genome
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3.7 years ago
gaoyanwang • 0

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

genome • 729 views
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3.7 years ago
 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).

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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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Entering edit mode
3.6 years ago
gaoyanwang • 0

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!