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Extract A Subrange Of Sequences From A Genbank File

Hi all,

I think the title explains it all. I have a Genbank flat file (a whole genome) and I want to have a new Genbank file containing only a range of the original file. So, if my genome is 1..3500000 in size I just want the sequences from 10000..20000, while maintaning the original annotation (genes, misc_features, etc) for this region, so the biggest problem is that coordinates have to be changed within the new Genbank file, since the new file should be in the 1..10000 range for this example.

I've searched for tools which could perform this task but have found none. Y'all have any ideas?

Thank you!

extraction genbank
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by Iván • Iván

Any other ideas?

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written by Iván • Iván

1 answer

if your sequence is available at the NCBI, you can go to genbank and view the record in the browser. On the right side there is a form "Change region shown". Update the record and then use the button "Send/Complete record" : "Destination=file" :"Format Genbank"

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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks, but the sequence is not available at any other DB!

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written by Iván • Iván

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