BLASTDB

Both the command line BLAST and the Galaxy Framework at UF HPC use the same BLAST databases. We retain two releases of the BLASTDB (blast databases) at a 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 or an out-of-cycle NCBI database update to be added 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. To ensure reproducibility of the analytical results within the time frame of an average bioinformatics project the BLAST databases are updated every three months and the old databases are kept around for one year.

BLASTDB releases

• Default - 2012-12 (Full mirror of NCBI Blast Databases).
• Also available
  • 2012-08 (Full mirror of NCBI Blast Databases).
  • 2012-05 (Full mirror of NCBI Blast Databases).

BLASTDB location

All databases are located in sub-directories of /bio/reference/blast. The default database is a /bio/reference/blastd/db symlink to the latest release directory. Its location is set automatically by the ncbi_blast module via the "$BLASTDB" variable.

Provided BLASTDB databases

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
• DROME_prot - Deep Metazoan Project protein database
• md5nr - A comprehensive non-redundant protein database
• Alligator.miss.v0.2 - Alligator mississippiensis v. 0.2 build
• PhumU1_USDA_sc - Pediculus humanus USDA suupercontigs
• p_schaeffi_v0_1_bboyd - Bret Boyd's build of the Pediculus Schaeffi genome
• vibrChol1 - Vibrio cholerae O1 biovar eltor str. N16961
• vibrChol_O395_1 - Vibrio cholerae O395
• vibrVuln_CMCP6_1 - Vibrio vulnificus CMCP6

NCBI

Protein:

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

Nucleotide:

• 16SMicrobial
• 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
• tsa_nt
• vector
• wgs