Question: How to set up Swissprot database for ncbi-blast+ using anaconda
0
gravatar for nazza2008
9 weeks 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 • 179 views
ADD COMMENTlink modified 9 weeks ago by h.mon23k • written 9 weeks ago by nazza20080
1
gravatar for h.mon
9 weeks ago by
h.mon23k
Brazil
h.mon23k 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 9 weeks ago • written 9 weeks ago by h.mon23k

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

ADD REPLYlink written 9 weeks 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 9 weeks ago by h.mon23k
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