biological-databases
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Table of Contents
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 20:12 by aorth