how to run blastp against nr databse locally

Question

[Arora]

I have downloaded the preformatted nr db using the below command and uncompressed all files to a folder. The folder contains multiple files such as nr.pto, nr.pot, nr.38.pog etc.

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

Executing the following command says blastp -query file.fasta -db nr -out results.out BLAST Database error: No alias or index file found for protein database [nr] in search path.

I tried doing makeblastdb -dbtype prot -in nr and it deleted all the files in my nr folder.

Is this the right step before executing a blastp?

[flogin]

normally to create a index file for blast databases I run:

makeblastdb -in file -dbtype prot

Answer 1

[gb]

You are missing an alias file, this is a text file that points to all those nr files. See this page for more info https://www.ncbi.nlm.nih.gov/books/NBK279693/

And also instead of wget you can use update_blastdb.pl --passive --decompress nr to download the full nr database. The script is included as part of the blast distribution.

If you do blastp -query file.fasta -db nr -out results.out make sure that the alias file is in your current folder. Otherwise it would be blastp -query file.fasta -db your/database/folder/nr -out results.out

The alias file name is nr.pal and is present in the last nr.tar.gz file

[Arora]

@gb Thank you I had the nr.pal file and I did as you suggested. Now it says Error:Not a valid version 4 database.

Do I have to run makeblastdb in nr folder before the blastp?

[Arora]

@gb Thank you I had the nr.pal file and I did as you suggested. Now it says Error:Not a valid version 4 database.

Do I have to run makeblastdb in nr folder before the blastp?

[gb]

No, you don't have to run makeblastdb. Are you using an old version of blast?

You can see that by doing blastp -version

You can either update blast, which is definitely the most recommended thing to do. Or you download the v4 database ftp://ftp.ncbi.nlm.nih.gov/blast/db/v4/

[Arora]

my version is blastp: 2.7.1+ Package: blast 2.7.1, build Mar 12 2018 19:11:30

[gb]

As far as I can find you need minimum 2.9.0

https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastNews

[Arora]

Yes thank you it was the version incompatibility. It works fine with the latest executables.

[GenoMax]

Be aware that v4 indexes are no longer being updated (after Feb 2020).

Answer 2

[brian.fristensky]

The entire process of installing BLAST databases and running BLAST searches is automated using the BioLegato applications found in the BIRCH system http://home.cc.umanitoba.ca/~psgendb. The following videos show BioLegato in action:

Installing BLAST databases on your own computer https://www.youtube.com/watch?v=R_gxDCXNUHY

BLAST Searches Through a Data Science Lens https://www.youtube.com/watch?v=Os3eKqXF4Mw