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The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

HPCC BLAST Repository

The HPCC has made 5 commonly used datasets available to BLAST users to permit searches.  BLAST formatted genomes included in the repository include those for human, mouse, and drosophila melanogaster, as well as the non-redundant protein sequence database (nr), and the nucleotide (nt) database.  The repository is located on the system in:

Related FASTA files are also provided in:

Installed Databases

BLAST-formatted databases currently installed on the HPCC as of the last update, include the following:

  1. human
  2. mouse
  3. drosophila melanogaster
  4. nr - Non-redundant protein sequence database with entries from GenPept, Swissprot, PIR, PDF, PDB, and NCBI RefSeq.
  5. nt
  6. refseq_protein
  7. uniref100
  8. Pfam-A
  9. Pfam-B

Using the Repository

To use the BLAST database repository, set the environmental variable BLASTDB as follows:

Also make sure to load the BLAST module to use the standalone version on the HPCC:

The repository is read-only and user-browsable.


Currently, the repository is updated manually on a somewhat irregular basis.  The last update is listed in the file:

To request a more recent update of any these genomes, please contact the HPCC.