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 twice a year around May 1st (Release #1) and November 1st (Release #2).

BLASTDB releases

• Default - 2012-05 (Full mirror of NCBI Blast Databases) - Release #1 of 2012.
• Legacy - 2012-02 (Subset of the NCBI Blast Databases).

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
• 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

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

2012-02 Release - a subset of NCBI BLAST databases:

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