BLASTDB: Difference between revisions
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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]. | 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 | * 2012-01 | ||
* 2012-02 | * 2012-02 | ||
* 2012-05 (Full mirror of NCBI Blast Databases) | * 2012-05 (Full mirror of NCBI Blast Databases) | ||
==Provided BLASTDB databases== | |||
===NCBI=== | |||
"2012-05" | "2012-05" | ||
| Line 60: | Line 60: | ||
* swissprot | * swissprot | ||
* wgs | * wgs | ||
===Custom=== | |||
* chlaCavGPIC | |||
* chlaPneumAR39 | |||
* chlaTracA | |||
* chlaTracD | |||
* chlaTracL2 | |||
* chlaTracMurNigg | |||
* md5nr | |||
Revision as of 21:37, 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
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