Difference between revisions of "BLASTDB"
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[[Category:Biology]][[Category:Bioinformatics]] | [[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 to be added | + | 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 twice a year around '''May 1st (Release #1)''' and '''November 1st (Release #2)'''. |
==BLASTDB releases== | ==BLASTDB releases== | ||
Revision as of 13:21, 8 May 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 - 2012-05 (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
NCBI
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 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