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 provide 3 recent monthly releases of the BLASTDB (blast databases). 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 | + | 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=== | ===Provided BLASTDB releases=== | ||
| − | |||
* 2012-01 | * 2012-01 | ||
* 2012-02 | * 2012-02 | ||
| + | * 2012-05 (Full mirror of NCBI Blast Databases) | ||
===Provided BLASTDB databases=== | ===Provided BLASTDB databases=== | ||
(Alphabetical listing) | (Alphabetical listing) | ||
| + | |||
| + | "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''': | '''2012-02''': | ||
Revision as of 21:23, 1 May 2012
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
(Alphabetical listing)
"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