BLASTDB

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