Question: How do I extract taxonomy/organism from NCBI .gb files?
0
gravatar for Ming
8 months ago by
Ming30
Ming30 wrote:

Hello there,

I am trying to extract the taxonomy section from the NCBI .gbk file. How do I go about doing so?

Thanks!

ncbi • 463 views
ADD COMMENTlink modified 8 months ago by Sej Modha4.2k • written 8 months ago by Ming30

For individual files that information is in the flat file. Are you trying to do this in a large scale? If so, what have you tried so far? Read up on Entrez Direct here: https://www.ncbi.nlm.nih.gov/books/NBK179288/ and you should be able to get started. Good luck!

ADD REPLYlink written 8 months ago by vkkodali1.1k
0
gravatar for Sej Modha
8 months ago by
Sej Modha4.2k
Glasgow, UK
Sej Modha4.2k wrote:

You can use this script that would parse any GenBank file with extension .gbff or .gbk in a specific location or present working directory and prints the sequence accession number and taxonomy ID.

ADD COMMENTlink modified 8 months ago • written 8 months ago by Sej Modha4.2k

Thank you! Will try it!

ADD REPLYlink written 8 months ago by Ming30
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