bacterial protein data from NCBI

Question

[Eva_Maria]

I want to do a local blast using all the bacterial protein data from NCBI. Is there any way to download all the data from NCBI?

Answer 1

[5heikki]

I would recommend that you just download the nr database with update_blastdb.pl and then pipe blastdbcmd output where you filter all bacterial GIs from nr to blastdb_aliastool. All these tools ship with blast. The taxonomy ID for Bacteria is "2". See here.