BLASTDB

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Both the command line BLAST and the Galaxy Framework at UF HPC use the same BLAST databases. We provide 3 recent monthly releases of the BLASTDB (blast databases) at any given time. The current BLASTDB version is made available to the ncbi_blast tools via the BLASTDB environment variable. Currently provided databases are listed below. If you need a custom database to be added to the list and would like to avoid using up your personal filespace quota please file a Support Request Ticket or contact the UF HPC Biological Computing Support.

Provided BLASTDB releases

  • 2012-01
  • 2012-02
  • 2012-05 (Full mirror of NCBI Blast Databases)

Provided BLASTDB databases

NCBI

"2012-05"

Protein:

  • env_nr
  • nr
  • refseq_protein
  • swissprot
  • pataa
  • pdbaa

Nucleotide:

  • 16SMicrobial
  • cdd_delta
  • env_nt
  • est
  • est_human
  • est_mouse
  • est_others
  • gss
  • htgs
  • human_genomic
  • human_genomic_transcript
  • mouse_genomic_transcript
  • nt
  • other_genomic
  • patnt
  • pdbnt
  • refseq_genomic
  • refseq_rna
  • refseqgene
  • sts
  • taxdb
  • tsa_nt
  • vector
  • wgs

2012-02:

  • est
  • est_human
  • est_mouse
  • st_others
  • nr
  • nt
  • other_genomic
  • refseq_genomic
  • refseqgene
  • refseq_protein
  • refseq_rna
  • swissprot
  • wgs

Custom

  • chlaCavGPIC - Chlamydia psittaci (GPIC)
  • chlaPneumAR39 - Chlamydia Pneumoniae
  • chlaTracA - Chlamydia trachomatis serovar A
  • chlaTracD - Chlamydia trachomatis serovar D
  • chlaTracL2 - Chlamydia trachomatis serovar L2
  • chlaTracMurNigg - Chlamydia muridarum
  • md5nr - A comprehensive non-redundant protein database