This is an old revision of the document!

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
nt	NCBI nucleotide collection (v5²)	Mar 24, 2020	`/export/data/bio/ncbi/blast/db/v5`
nr	NCBI protein collection (v5²)	Mar 24, 2020	`/export/data/bio/ncbi/blast/db/v5`
UniProt's UniProtKB/Swiss-Prot	Manually curated, most reliable	2019-07-01	`/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

Tools like BLAST use the BLASTDB environment variable to find the location of the system's BLAST databases. ILRI's BLAST environment modules like blast/2.10.0+ automatically set this variable when you load the module.

If you are using different software you will need to set the variable manually, for example:

$ export BLASTDB=$BLASTDB:/export/data/bio/ncbi/blast/db/v5
$ blastn -db nt -query file.seq -out blast.out

Notes

1. Use the following to determine the date of a BLAST database:

$ module load blast/2.10.0+
$ blastdbcmd -info -db nt | grep Date

2: NCBI introduced database format version 5 in 2019 and these only work with BLAST tools starting from 2.9.0. They are no longer updating the version 4 databses, but we have preserved them in a separate directory if you are using tools that do not support version 5.