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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 Where it resides How to use
NCBI nr/nt nucleotide collectionN/A2018-11-24/export/data/bio/ncbi/blast/dbuse BLASTDB=/export/data/bio/ncbi/blast/db and blastn … -db nt in your Bash script
NCBI nr/nt protein collectionN/A2018-08-16/export/data/bio/ncbi/blast/dbuse 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/dbuse BLASTDB=/export/data/bio/uniprot/blast/db 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

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.1552506137.txt.gz · Last modified: 2019/03/13 22:42 by aorth