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
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nazza2008 •
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
Do we need to create an environment variable $BLASTDB to point to the directory where we want to store our database?
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.
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