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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	Version Number	Last Updated¹	Where it Resides	How to Use
NCBI nr/nt nucleotide collection	N/A	2018-11-24	`/export/data/bio/ncbi/blast/db`	Use `BLASTDB=/export/data/bio/ncbi/blast/db` and `blastn … -db nt` in your Bash script
NCBI nr/nt protein collection	N/A	2018-08-16	`/export/data/bio/ncbi/blast/db`	use `BLASTDB=/export/data/bio/ncbi/blast/db` and `blastp … -db nr` in your Bash script
UniProt's UniProtKB/Swiss-Prot (manually curated, most reliable)	N/A	?	`/export/data/bio/uniprot/blast/db`	use `BLASTDB=/export/data/bio/uniprot/blast/db` in your Bash script
UniProt's UniProtKB/TrEMBL (automated curation)	N/A	?	`/export/data/bio/uniprot/blast/db`	use `BLASTDB=/export/data/bio/uniprot/blast/db` in your Bash script
UniProt's UniRef100	N/A	?	`/export/data/bio/uniprot/blast/db`	use `BLASTDB=/export/data/bio/uniprot/blast/db` in your Bash script

Footnotes

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