Getting gene identifier (GI) IDs from NCBI nr database

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

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updated 3.6 years ago by Ram

• written 11.2 years ago by Prasad •

1 answer

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

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updated 3.6 years ago by Ram

• written 11.2 years ago by GenoMax

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.

• 0 views • link

updated 3.6 years ago by Ram

• written 11.2 years ago by Prasad •

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