View source for BLASTDB

[[Category:Biology]][[Category:Bioinformatics]]
Both the [[Blast|command line BLAST]] and the [[Galaxy|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 <code>BLASTDB</code> 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 [http://support.hpc.ufl.edu Support Request Ticket] or contact the [mailto:bio@hpc.ufl.edu 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
* chlaPneumAR39
* chlaTracA
* chlaTracD
* chlaTracL2
* chlaTracMurNigg
* md5nr