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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 collectionN/A24 Nov 2018/export/data/bio/ncbi/blast/dbuse BLASTDB=/export/data/bio/ncbi/blast/db in your Bash script
NCBI nr/nt protein collectionN/A16 Aug 2018/export/data/bio/ncbi/blast/dbuse BLASTDB=/export/data/bio/ncbi/blast/db and blastn … -db nt in your Bash script
UniProt's UniProtKB/Swiss-Prot (manually curated, most reliable)N/A?/export/data/bio/uniprot/blast/dbuse BLASTDB=/export/data/bio/uniprot/blast/db and blastp … -db nr in your Bash script
UniProt's UniProtKB/TrEMBL (automated curation)N/A?/export/data/bio/uniprot/blast/dbuse BLASTDB=/export/data/bio/uniprot/blast/db in your Bash script
UniProt's UniRef100N/A?/export/data/bio/uniprot/blast/dbuse BLASTDB=/export/data/bio/uniprot/blast/db in your Bash script
biological-databases.1552385675.txt.gz · Last modified: 2019/03/12 10:14 by jean-baka