Question: How to set up Swissprot database for ncbi-blast+ using anaconda
0
gravatar for nazza2008
6 months ago by
nazza20080
nazza20080 wrote:

Hello, I'm trying to install ncbi-blast+ with SwissProt database using anaconda. I already install the ncbi-blast+ package, how to I setup the database? I'm on ubuntu 18.04

blast anaconda ubuntu ncbi • 331 views
ADD COMMENTlink modified 6 months ago by h.mon26k • written 6 months ago by nazza20080
1
gravatar for h.mon
6 months ago by
h.mon26k
Brazil
h.mon26k wrote:

The same way you set up any Blast+ database: download the fasta file and build the Blast+ database:

wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz
gunzip uniprot_sprot.fasta.gz
makeblastdb -in uniprot_sprot.fasta -out uniprot_sprot -type prot
ADD COMMENTlink modified 6 months ago • written 6 months ago by h.mon26k

Do we need to create an environment variable $BLASTDB to point to the directory where we want to store our database?

ADD REPLYlink written 6 months ago by nazza20080

You don't need to set up $BLASTDB. For example, my databases are scattered all over - most of them are project-specific - and I just pass the whole path to the database.

However, it will be helpful to set $BLASTDB if you have a lot of databases at the same location, or if you want to have lots of different locations available to Blast without complications.

ADD REPLYlink written 6 months ago by h.mon26k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1718 users visited in the last hour