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, etc. Below you can find the list of them, their source URL and the last time they were updated, with links to the update scripts that our system administrator use to perform updates.
We endeavor to keep this list updated as the One True List™.
| Name | Version number | Last updated | Where it resides | How to use |
|---|---|---|---|---|
| NCBI nr/nt nucleotide collection | N/A | 24 Nov 2018 | /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 | 16 Aug 2018 | /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 |
biological-databases.1552385713.txt.gz · Last modified: 2019/03/12 10:15 by jean-baka