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What is GeneDB?

Funded as part of the Wellcome Trust Functional Genomics Development Initiative, the GeneDB project is aiming to develop and maintain curated database resources for three organisms: Schizosaccharomyces pombe, which has been completely sequenced, and the kinetoplastid protozoa Leishmania major and Trypanosoma brucei, whose genome sequences have yet to be completed. The goals are to capture, store and manage data for integration with emerging functional genomics and proteomics projects and to provide an easy-to-use, user-friendly interface, including a variety of graphical displays. It is envisaged that the generic database structure will subsequently be adopted to integrate datasets for other organisms, both prokaryotic and eukaryotic, that have been sequenced by the Sanger Institute Pathogen Sequencing Unit. To this extend, datasets for Saccharomyces cerevisiae as well as the filamentous fungus Aspergillus fumigatus are already available through GeneDB. The database has been developed through close collaboration between Sanger Institute software developers, on-site organism specific curators and representatives of the research communities. The data within geneDB are manually annotated and curated, frequently updated and, because of the structured annotation and use of controlled vocabulary, easy to precisely query. The database is under constant review and new functionality will be added as it evolves.

What are the various ways to search GeneDB?

GeneDB provides users with the following information, functionality and research tools. The following are descriptions of ways to search GeneDB, where links will take you to the relevant areas of the database or to example pages. All the relevant search pages are available from a database entry point on both the GeneDB homepage and the individual organism homepages.

Menu Bar (Screenshot)

To aid in the navigation of the site a menu bar is available on the pages within GeneDB. Most of the options available on GeneDB frontpages are featured together with a comprehensive glossary of useful terms and databases. The menu bar has a gene search box, a drop down menu for the other organisms within GeneDB, Blast search and a link to the main search page. Also available are links to the GeneDB and organism frontpages via the prominant GeneDB logos above the menu bar.

Searching for a gene by name or synonym (Screenshot)

This option is also available on the menu bar of each gene page. Entering a gene name or synonym will lead either directly to the relevant gene page (eg dld1 in S. pombe) if a specific unique term is used or to a list of genes including that term (eg *kinase* in T. brucei and L. major) if a wild card is used. A list of genes will provide links to each relevant gene page.

Browsing by catalogues (Screenshot)

The list of browsable terms includes

• products/description: This brings up a gene product list with links to relevant gene pages for each product
• SWISS-PROT keywords: This is a browsable list of SWISS-PROT keywords assigned by SWISS-PROT curators to a given protein linking to the relevant gene or gene list pages
• GO (Gene Ontology) list: This allows the user to search for genes by classification of their respective products into molecular function, biological process and cellular component using the controlled vocabulary defined by the GO consortium.
• Pfam (domain data): This is a list of protein domain families defined by sequence alignments and hidden Markov models.

Sequence searching using BLAST (Screenshot)

The BLAST and omniBLAST links lead to self-explanatory search pages, allowing users to paste in any nucleotide or amino acid sequence and compare it for similarity to any sequence within the database. Results are returned either directly or by e-mail.

Full text search (Screenshot)

Search the whole site for any text reference using a web-based search engine. This option is available via the main search page link in the database entry point of each front page. A full text search box allows for searches across all the organisms within the database or just for a selected organism chosen from a drop down menu.

What kinds of information are in GeneDB?

Central to GeneDB are the gene pages, providing a comprehensive annotation of genes within each organism with:

• Access DNA and protein sequences of protein coding genes with the ability of sending sequences straight to the associated BLAST servers
• Predicted peptide properties (including signal peptide and transmembrane predictions)
• Similarity information (EMBL, SWISS-PROT including annotation)
• Gene ontology (GO) annotation
• Summary of up-to-date protein domain and motif searches (InterPro, Pfam, PRINTS, PROSITE, BLOCKS, SMART)
• Literature links
• SWISS-PROT annotation

How to cite GeneDB?

Please cite GeneDB by the paper.

 

Contacting us/sending us feedback

Thank you for trying GeneDB. As we aim to continually update, modify and develop our information resource in response to the needs of the community, GeneDB welcomes comments, suggestions and feedback . Please send questions about use of GeneDB services or comments about GeneDB to us. We provide a number of different forms to contact us, depending upon the exact nature of your suggestion/problem/complaint. They are:

1. General comments about the site
   Every page has a link at the bottom of the right hand corner which takes you to a feedback form. Please use this for general comments about the website itself such as how easy it is to find the section you want, any display problems on your particular browser, unfriendly error messages or any other queries that are of a more technical nature.
2. Comments about a particular gene
   If you wish to contribute additional information on a gene and/or corrections to the provided summary or new data that will not be included in a journal publication, then please do so. Each gene page has a link at the top and bottom giving access to a feedback form for that particular gene. This allows you to quickly and easily inform the curator of any information that you think is relevant to this gene.
3. General comments about a particular organism
   Each organism homepage has a link at the bottom (in the centre) contacting the curator. The various annotators/curators are:
   
   

   A. fumigatus	Matthew Berriman (mb4@sanger.ac.uk)
   S. cerevisiae	Valerie Wood (val@sanger.ac.uk)
   S. pombe	Valerie Wood (val@sanger.ac.uk)
   L. major	Chris Peacock (csp@sanger.ac.uk) and Al Ivens (alicat@sanger.ac.uk)
   T. brucei	Christiane Hertz-Fowler (chf@sanger.ac.uk) and Matthew Berriman (mb4@sanger.ac.uk)
   P. falciparum	Andrew Berry (aeb@sanger.ac.uk) and Matthew Berriman (mb4@sanger.ac.uk)

   
   

   Data from individuals will be curated by GeneDB as 'Personal communication to GeneDB from '.

Some stats about GeneDB

Data being prepared

 

GeneDB Privacy policy

We encourage the submission of additional information and expertise by the community, and will accordingly publicly credit said individuals/institutes as having contributed these data, if displayed on the WWW as part of GeneDB. This will not constitute publication. In the interests of privacy, contact details of the contributor will, however, not be made public, nor passed on to others without the express permission of the contributor.

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