Bioinformatics Databases

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	02/22/2017	Sapelo2
Uniprot	02/15/2013	Zcluster
Uniref	02/22/2017	Sapelo
Uniref	02/22/2017	Sapelo2
Uniref	01/07/2015	Zcluster
wublast		Zcluster
wublast		Sapelo2