GenomeMine

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About

About GenomeMine

The GenomeMine database contains information about published genomes from eukaryotes, bacteria, plasmids, organelles, and viruses.

Under Construction

The database is currently under construction. Any problems should be reported to curator at ceh.ac.uk. We are working on GenomeMine II which should be released around October.

Notes on Database

The information in the GenomeMine has been obtained from a variety of sources. A list of all the contributed data sets can be viewed under Datasets.

The GenomeMine "Genomic Features" Datasets

Contributed datasets can contain attributes for any number of complete genomes from any taxonomic group. The GenomeMine therefore aims to hold basic information about every complete genome by maintaining its own "Genomic Features" datasets for different taxa. These datasets are generated by periodically updating our complete genomes list from the NCBI Entrez Genomes database and the Genomes Online Database (GOLD). This dataset is currently divided into 3 subsets of genomes "bacteria", "organelles, plasmids, and viruses", and "eukaryotes". Each non-eukaryotic genome annotation file is then parsed to extract and calculate a basic set of information. The eukaryotic data is manually collected from the primary genome report of each organism. This is currently the only data set that can be searched using the Search page, but the GenomeMine II release should allow expanded search capabilities.

Updates

Datasets are being added to the GenomeMine as they are contributed. Datasets are also periodically updated to contain additional genomes or improved content. To contribute a data set please contact us through curator at ceh.ac.uk

Linking to GenomeBank

It is possible to link the GenomeBank to view a list of attributes stored for each genome if you know the NCBI RefSeq identifier (or CMR alias for bacterial genomes) for your genome. To do so, use the following base URL, replacing ?NC_000854? with the identifier of your genome.

http://www.genomics.ceh.ac.uk/cgi-bin/genomemine/gminemenu.cgi?action=genomebank&nc=NC_000854

GenomeMine Contacts

The GenomeMine database was conceived and developed by Dawn Field (dfield at ceh.ac.uk) and Jennifer Hughes (Jennifer_B_Hughes at brown.edu).

Other Contributors:

Tanya Gray	GenomeMine interface and database development
Gareth Wilson	Curation of bacterial genomes from NCBI
Adrian Tett	Curation of plasmid genomes from NCBI, images
Milo Thurston	Curation of viral and organellar genomes from NCBI
John Day	images