Difference between revisions of "BLASTDB"
Moskalenko (talk | contribs) |
Moskalenko (talk | contribs) |
||
| Line 3: | Line 3: | ||
==BLASTDB releases== | ==BLASTDB releases== | ||
| − | * Default - 2012- | + | * Default - 2012-12 (Full mirror of NCBI Blast Databases). |
* Also available | * Also available | ||
| + | **2012-08 (Full mirror of NCBI Blast Databases). | ||
**2012-05 (Full mirror of NCBI Blast Databases). | **2012-05 (Full mirror of NCBI Blast Databases). | ||
| − | |||
==Provided BLASTDB databases== | ==Provided BLASTDB databases== | ||
| Line 22: | Line 22: | ||
* PhumU1_USDA_sc - Pediculus humanus USDA suupercontigs | * PhumU1_USDA_sc - Pediculus humanus USDA suupercontigs | ||
* p_schaeffi_v0_1_bboyd - Bret Boyd's build of the Pediculus Schaeffi genome | * 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=== | ===NCBI=== | ||
| Line 56: | Line 59: | ||
* vector | * vector | ||
* wgs | * wgs | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
Revision as of 19:50, 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. 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 - 2012-12 (Full mirror of NCBI Blast Databases).
- Also available
- 2012-08 (Full mirror of NCBI Blast Databases).
- 2012-05 (Full mirror of NCBI Blast Databases).
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