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biological-databases

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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 Database Location 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

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 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

biological-databases.1552507948.txt.gz · Last modified: 2019/03/13 23:12 by aorth