Difference between revisions of "BLASTDB"

Revision as of 19:54, 5 December 2012

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

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

@@ Line 1: / Line 1: @@
 [[Category:Biology]][[Category:Bioinformatics]]
-Both the [[Blast|command line BLAST]] and the [[Galaxy|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 <code>BLASTDB</code> 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 [http://support.hpc.ufl.edu Support Request Ticket] or contact the [mailto:bio@hpc.ufl.edu 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.
+Both the [[Blast|command line BLAST]] and the [[Galaxy|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 <code>BLASTDB</code> 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 [http://support.hpc.ufl.edu Support Request Ticket] or contact the [mailto:bio@hpc.ufl.edu 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==