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GeneDB


NAR Molecular Biology Database Collection entry number 328
The GeneDB Team
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK

Database Description

GeneDB (http://www.genedb.org/) is a genome database, housing sequence and annotation from a diverse range of organisms. The resource aims to provide intuitive access to data generated by the WTSI Pathogen Sequencing Unit (http://www.sanger.ac.uk/Projects/Pathogens/) and its collaborators. Over the past year, the number and range of organisms in GeneDB has continued to increase, now totalling 33 datasets, including representatives from two new taxa - viruses and parasitic helminths. In addition, GeneDB is designed to store data from both initial shotgun projects with automated annotation through to completed genomes. Four of the organism datasets, (S. pombe, P. falciparum, T. brucei and L. major), are being actively curated with weekly updates to sequence and annotation.

As many of the datasets in GeneDB are from organisms that cause devastating diseases in the developing world, a stand alone version of GeneDB has been produced for CD distribution of a sub-set of the data. The CD supports all the core searching and display functions of the site and is particularly aimed at increasing access for researchers in endemic countries. (A Tri-tryp CD is freely available via http://www.who.int/tdr/media/multimedia/trypanosomatids.htm ).

Recent Developments

Recent developments have concentrated on both extending the curated information captured and cross-linked on the feature pages, and the addition of new tools for data retrieval, browsing and searching. A simple form based system has been implemented to bulk download sequence and annotations. This can use input from either i) the query history, ii) browsable catalogues or iii) user defined lists. The Artemis genome browser [2] has been updated to the latest release. A complementary view of the sequence and annotation is now also available via the newly implemented Gbrowse [2]. Iterative PSI-BLAST [4] searches both against the datasets stored within GeneDB as well as against the UniProt public protein database are now also available.

References

1. Christiane Hertz-Fowler, Chris S. Peacock, Valerie Wood, Martin Aslett, Arnaud Kerhornou, Paul Mooney, Adrian Tivey, Matthew Berriman, Neil Hall, Kim Rutherford, Julian Parkhill, Alasdair C. Ivens, Marie-Adele Rajandream and Bart Barrell. GeneDB: a resource for prokaryotic and eukaryotic organisms. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D339-D343.
2. K. Rutherford, J. Parkhill, J. Crook, T. Horsnell, P. Rice, M-A. Rajandream and B. Barrell (2000) Artemis: sequence visualisation and annotation. Bioinformatics 16 (10) 944-945.
3. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S. The generic genome browser: a building block for a model organism system database. Genome Res. 2002 Oct;12(10):1599-610.
4. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ.Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389-402.


Go to the abstract in the NAR 2012 Database Issue.
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