Getting gene identifier (GI) IDs from NCBI nr database

Question

[Prasad]

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.

Answer 1

[GenoMax]

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

[Prasad]

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.