BLASTDB: Difference between revisions

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[[Category:Biology]][[Category:Bioinformatics]]
[[Category:Biology]][[Category:Data]]
Both the [[Blast|command line BLAST]] and the [[Galaxy|Galaxy Framework]] at UFRC 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.rc.ufl.edu Support Request Ticket] or contact the [mailto:bio@rc.ufl.edu UFRC 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 "$BLASTDB" variable in the job script or by selecting the appropriate database in the BLAST interface in the Galaxy.
Both the [[Blast|command line BLAST]] and the [[Galaxy|Galaxy Framework]] at UFRC use the same BLAST databases. We retain two releases of the BLASTDB (blast databases) at a time. The current BLASTDB version is made available to the ncbi_blast tools via the <code>BLASTDB</code> environment variable. Currently provided databases are listed below. If you need a custom database or an out-of-cycle NCBI database update to be added and would like to avoid using up your personal filespace quota please file a [http://support.rc.ufl.edu Support Request Ticket] or contact the [mailto:bio@rc.ufl.edu UFRC Biological Computing Support]. The BLAST databases are updated every three months. However, to ensure reproducibility of the BLAST results within the time frame of an average bioinformatics project two old database releases are kept and can be accessed by setting the "$BLASTDB" variable in the job script or by selecting the appropriate database in the BLAST interface in the Galaxy.


=NCBI BLASTDB releases=
=NCBI BLASTDB releases=
*2018-01 (Full mirror) - '''default database'''.
All databases are full mirrors of NCBI data
*2017-01 (Full mirror)
* 202404 - '''default'''
*2016-07 (Full mirror)
* 202304
*2015-12 (Full mirror)
* 202112
*2015-06 (Full mirror)
*2014-11 (Full mirror)
*2014-04 (Full mirror)


=BLASTDB location=
=BLASTDB location=
All databases are located in sub-directories of <code>/ufrc/data/reference/blast</code>. The default database directory is a symlink to the latest release, but the older releases are still available. Its location is set automatically by the ncbi_blast module via the "$BLASTDB" variable. To override the default database location to perhaps use the older release run <code>'export BLASTDB=/some/path'</code> either on the command line or in the job script as appropriate. E.g. <code>'export BLASTDB=/ufrc/data/reference/blast/201506'</code>. Afterwards, continue calling databases by name without the full path. For example, 'blastx -db nr ...'.
All databases are located in sub-directories of <code>/data/reference/blast</code>. The default database directory is a symlink to the latest release, but the older releases are still available. Its location is set automatically by the ncbi_blast module via the "$BLASTDB" variable. To override the default database location to perhaps use the older release run <code>'export BLASTDB=/some/path'</code> either on the command line or in the job script as appropriate. E.g. <code>'export BLASTDB=/data/reference/blast/201506'</code>. Afterwards, continue calling databases by name without the full path. For example, 'blastx -db nr ...'.


=Provided BLASTDB databases=
=Provided BLASTDB databases=
 
===Default BLASTDB===
<div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 1px solid gray;">
''Expand this section to view list of NCBI Databases.''
<div class="mw-collapsible-content" style="padding: 5px;">
<pre>
16S_ribosomal_RNA
18S_fungal_sequences
28S_fungal_sequences
Betacoronavirus
ITS_RefSeq_Fungi
ITS_eukaryote_sequences
LSU_eukaryote_rRNA
LSU_prokaryote_rRNA
SSU_eukaryote_rRNA
cdd_delta
env_nr
env_nt
human_genome
landmark
mito
mouse_genome
nr
nt
pataa
patnt
pdbaa
pdbnt
ref_euk_rep_genomes
ref_prok_rep_genomes
ref_viroids_rep_genomes
ref_viruses_rep_genomes
refseq_protein
refseq_rna
refseq_select_prot
refseq_select_rna
swissprot
taxdb
tsa_nr
tsa_nt
</pre></div></div>
==Custom==
==Custom==
<div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 1px solid gray;">
''Expand this section to view list.''
<div class="mw-collapsible-content" style="padding: 5px;">
* Alligator.miss.v0.2 - Alligator mississippiensis v. 0.2 build
* Alligator.miss.v0.2 - Alligator mississippiensis v. 0.2 build
* Aliivibrio Fischeri (ASM1180v1)
* Aliivibrio Fischeri (ASM1180v1)
Line 62: Line 101:
* vibrChol_O395_1 - Vibrio cholerae O395
* vibrChol_O395_1 - Vibrio cholerae O395
* vibrVuln_CMCP6_1 - Vibrio vulnificus CMCP6
* vibrVuln_CMCP6_1 - Vibrio vulnificus CMCP6
 
</div></div>
===NCBI===
__NOTOC__
 
'''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

Latest revision as of 18:52, 10 April 2024

Both the command line BLAST and the Galaxy Framework at UFRC 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 UFRC 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.

NCBI BLASTDB releases

All databases are full mirrors of NCBI data

  • 202404 - default
  • 202304
  • 202112

BLASTDB location

All databases are located in sub-directories of /data/reference/blast. The default database directory is a symlink to the latest release, but the older releases are still available. Its location is set automatically by the ncbi_blast module via the "$BLASTDB" variable. To override the default database location to perhaps use the older release run 'export BLASTDB=/some/path' either on the command line or in the job script as appropriate. E.g. 'export BLASTDB=/data/reference/blast/201506'. Afterwards, continue calling databases by name without the full path. For example, 'blastx -db nr ...'.

Provided BLASTDB databases

Default BLASTDB

Expand this section to view list of NCBI Databases.

Custom

Expand this section to view list.

Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=BLASTDB&oldid=28490"