Bioinformatics Databases: Difference between revisions
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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. | 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 "/work/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 | Of the public local databases in /work/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. | 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. | ||
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| [[wublast-Sapelo2|wublast]] || || [[:Category:Sapelo2|Sapelo2]] | | [[wublast-Sapelo2|wublast]] || || [[:Category:Sapelo2|Sapelo2]] | ||
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| [[decontaMiner-Sapelo2|decontaMiner]] || 08/30/2019 || [[:Category:Sapelo2|Sapelo2]] | |||
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Revision as of 08:35, 30 August 2019
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 "/work/db" filesystem.
Of the public local databases in /work/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 |
|---|---|---|
| Bacteria NCBI | 12/21/2017 | Sapelo2 |
| gss | Sapelo2 | |
| htgs | Sapelo2 | |
| hg | Sapelo2 | |
| NCBI BLAST Database | every other month | Sapelo2 |
| NCBI Fasta | every other month | Sapelo2 |
| pfam | 27.0 | Sapelo2 |
| Refseq | Sapelo2 | |
| TaxDB | Sapelo2 | |
| Uniprot | 06/28/2018 | Sapelo2 |
| Uniref | 06/28/2018 | Sapelo2 |
| wublast | Sapelo2 | |
| decontaMiner | 08/30/2019 | Sapelo2 |