Question: Extract A Subrange Of Sequences From A Genbank File
gravatar for Iván
8.6 years ago by
Iván20 wrote:

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 • 1.9k views
ADD COMMENTlink written 8.6 years ago by Iván20

Any other ideas?

ADD REPLYlink written 8.6 years ago by Iván20
gravatar for Pierre Lindenbaum
8.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

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"

ADD COMMENTlink written 8.6 years ago by Pierre Lindenbaum129k

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

ADD REPLYlink written 8.6 years ago by Iván20
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