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Biological Sequence Databases on the HPC

Some of the most common biological sequence databases are available on the HPC for you to use with tools like BLAST. Below you can find the list of them, their location on the system, and the last time they were updated.

We endeavor to keep this list updated as the One True List™.

Name	Comments	Updated¹	Database Location
nr/nt	NCBI nucleotide collection	2019-06-20	`/export/data/bio/ncbi/blast/db`
nr/nt	NCBI protein collection	2019-06-20	`/export/data/bio/ncbi/blast/db`
UniProt's UniProtKB/Swiss-Prot	Manually curated, most reliable	?	`/export/data/bio/uniprot/blast/db`
UniProt's UniProtKB/TrEMBL	Automated curation	?	`/export/data/bio/uniprot/blast/db`
UniProt's UniRef100		?	`/export/data/bio/uniprot/blast/db`

Using These Databases

To use these databases you generally need to set an environment variable pointing to the location of the database before running your program. For example, to use nt with NCBI blastn:

$ export BLASTDB=/export/data/bio/ncbi/blast/db
$ blastn -db nt -query file.seq -out blast.out

Notes

¹ Use the following to determine the date of a BLAST database: /export/apps/blast/2.7.1+/bin/blastdbcmd -info -db nt | grep Date