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. The BLAST databases are updated every three months. However, to ensure reproducibility of the BLAST results within the time frame of an average bioinformatics project two old database releases are kept and can be accessed by setting the "$BLASTDB" variable in the job script or by selecting the appropriate database in the BLAST interface in the Galaxy.

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

• Alligator.miss.v0.2 - Alligator mississippiensis v. 0.2 build
• a_baumannii-AB0057 - A. baumannii str. AB0057
• aplCal3 - A. californica 3.0 WGS assembly, 4331 contigs
• 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
• lsu108 - LSURef - large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya), release 108.
• lsu111 - LSURef - large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya), release 111 (July 2012).
• md5nr - A comprehensive non-redundant protein database
• m_tuberculosis-CDC1551 - M. tuberculosis str CDC1551
• PhumU1_USDA_sc - Pediculus humanus USDA suupercontigs
• p_schaeffi_v0_1_bboyd - Bret Boyd's build of the Pediculus Schaeffi genome
• rfam_10_1 - release 10.1 of the Rfam collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs).
• rfam_11 - release 11 (August 2012, 2208 families) of the Rfam collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs).
• rn5 - Ratticus norvegicus rn5 release
• s_enterica-P125109 - S. enterica str P125109
• ssu108nr - SSURef NR - small (16S/18S, SSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya), release 108.
• ssu111nr - SSURef NR - small (16S/18S, SSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya), release 111 (July 2012).
• 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