Bioinformatics Databases

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As part of our services, the GACRC builds and hosts local copies of frequently cited application data, and provides assistance for sharing data among GACRC members, in the commonly shared "/db" filesystem.

Of the public local databases in /db, NCBI's nr and nt datasets are the most commonly used at the GACRC. GACRC staff will update these datasets every other month in fasta format. From these updated datasets, we will also build NCBI Blast and WUBlast databases in both nucleotide and protein formats.

Various subject datasets, e.g. pfam, bowtie indexes of human and mouse, and NCBI bacterial datasets, are hosted as well. These datasets either don’t need updating, the source does not update frequently, or the datasets are not used frequently by our users. These datasets will only be updated by user request.

For datasets requested by individual lab groups, GACRC staff will assist in setting up a group-shared environment and request that group members maintain their database files there.

For datasets frequently updated by their source, the GACRC encourages users to maintain their own copies of these public databases.

The set of data which are regularly updated is open to review, and can be expanded based on available GACRC resources.


Installed Bioinformatics Databases

Name Version Cluster
Arabidopsis Zcluster
Arb Zcluster
Bacteria NCBI 12/21/2017 Sapelo
BWA Zcluster
COG Zcluster
FISH Zcluster
gss Sapelo2
htgs Sapelo2
hg Sapelo2
KEGG Zcluster
maize 09/02/2014 Zcluster
Medicago Zcluster
Microbial 06/2013 Zcluster
NCBI BLAST Database every other month Sapelo
NCBI BLAST Database every other month Sapelo2
NCBI BLAST Database every other month Zcluster
NCBI Fasta every other month Sapelo
pfam 27.0 Zcluster
pfam 27.0 Sapelo2
Populus Zcluster
Refseq Sapelo2
Refseq Zcluster
RNA Seq Zcluster
Rice TIGR Zcluster
Roseobacter Zcluster
Silva Zcluster
Soybean 03/20/2013 Zcluster
Sus_scrofa Zcluster
TaxDB Sapelo2
TAIR-Sapelo TAIR10 Zcluster
Uniprot 02/22/2017 Sapelo
Uniprot 06/28/2018 Sapelo2
Uniprot 02/15/2013 Zcluster
Uniref 02/22/2017 Sapelo
Uniref 06/28/2018 Sapelo2
Uniref 01/07/2015 Zcluster
wublast Zcluster
wublast Sapelo2