How to update or install your local NCBI BLAST database in a Unix shell using update_blastdb.pl

I recently updated my local BLAST database and I thought I would revisit the process of installing/updating, but this time using the included update_blastdb.pl script.

First,  make sure the BLAST program is set to your path.  Because I work on a cluster all I  do is load the module.

 
module load bio/blast+/2.7.1

I then delete the old database folder and make a new folder with the same exact name (this keeps your old  scripts working ). If you are doing a fresh install, just create a new folder.

 
module load bio/blast+/2.7.1 
rm -r blastdb_folder_name
mkdir blastdb_folder_name

Now use the perl script to download the database of your choice.  The decompress option automatically decompresses the tar.gz files. Depending on what database you choose to download and your internet speeds, this could be a lengthy process.

 
perl update_blastdb.pl --decompress nt

I am also downloading the taxonomy database to know more about my BLAST hits. You have to manually unpack this database.

 
module load bio/blast+/2.7.1 
perl update_blastdb.pl taxdb
gunzip taxdb.tar.gz 

That’s it! Now you should have an updated BLAST database.

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