How many nr database subdirectories are there?

Question

[Jessica]

Hi,

I am trying to download the blast nr database into my HPCC account to be blast some files. When I downloaded the nr database and tried to manually build the database, it took so long that the HPCC killed the job. Next I tried to download the subdirectories of the nr database.

wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*tar.gz

I have been downloading these files all day. I am currently at nr.59.tar.gz and it is still downloading. Does anyone know how many subdirectories will be downloaded?

Thanks in advance!

[Andrzej Zielezinski]

There are 59 files for download in total :) If your query sequence set is small, you can run blast without downloading the nr database: blastp -query query.fasta -db nr -remote.

Answer 1

[GenoMax]

There are 59 (+1 nr.pal) files for nr database (not sub-directories) as of today. This set of database files are already formatted. All you need to do is keep all nr* files in one directory after you uncompress them. Set $BLASTDB variable to point to that directory and then use for blast.