Question: Getting gene identifier (GI) IDs from NCBI nr database
0
gravatar for Prasad
4.7 years ago by
Prasad 30
United States
Prasad 30 wrote:

I have  NCBI nr database. I would like to retrieve all the Gene Identifier (GI) IDs from it.

Which will be best way to do it? Does 'blastbdcmd' has any function which can help me get the desired results ?

Any guidance is greatly appreciated.

blast biopython • 1.8k views
ADD COMMENTlink modified 4.7 years ago by genomax78k • written 4.7 years ago by Prasad 30
1
gravatar for genomax
4.7 years ago by
genomax78k
United States
genomax78k wrote:

This should work. May take a while since nr is a large database.

$ blastdbcmd -entry 'all' -db /path_to/nr -outfmt '%g' -out result_file
ADD COMMENTlink written 4.7 years ago by genomax78k

Thanks for quick reply. It worked for me when I tested on test database. But ya as you said it's taking forever to run on nr database.

ADD REPLYlink written 4.7 years ago by Prasad 30
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