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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 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 and blastn … -db nt 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 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
biological-databases.1552505595.txt.gz · Last modified: 2019/03/13 22:33 by aorth