GeneDB: A database for Prokaryotic and Eukaryotic Organisms

1. GeneDB: A database for Prokaryotic and Eukaryotic Organisms Pathogen Sequencing Unit The Wellcome Trust Sanger Institute

2. Pathogen Sequencing Unit (http://www.sanger.ac.uk/Projects/) The Pathogen Group is funded to sequence the genomes of a wide range of prokaryotic and eukaryotic organisms Yeasts and Fungi: Schizosaccharomyces pombe Aspergillus fumigatus Pneumocystis carinii Bacteria: M. tuberculosis M. leprae Y. pestis S. typhi C. diphtheria B. pseudomallei Protozoa: Plasmodium falciparum Leishmania Trypanosoma Eimeria Theileria

3. Sanger Institute Project pages Sequence databases (EMBL, Genbank, Swiss-Prot) Analysis FTP site BLAST GeneDB Dissemination of information sequence and annotation

4. Literature searches User data submissions and updates 10 sequence databases Curated protein databases validation value addition Gene Ontology Protein domain databases Gene prediction tools Database searches Organism databases Functional genomics resources Protein motif predictions cross-references submissions/updates reports flatfiles GeneDB serialised objects ftp GUS tools Java Servlets/JSP classes Motif search EMOWSE BLAST links to feature pages sequence annotation curation GeneDB mining code

6. Basic information • Location c) Curated annotation • Predicted peptide properties

7. Database cross references • Gene Ontology: annotation • using the GO controlled vocabulary • Curated orthologs • Similarity information • Swiss-Prot annotations • Contact details

8. Curation within GeneDB • 1 curator per organism/related species • maintenance of sequence data / annotation • of multi-centre of often unfinished projects • integration of information extracted from • literature, public databases, community • feedback using structured syntax/vocabulary • nomenclature

10. (PMID:12574127)

11. Databases Martin Aslett Andy Berry Christiane Hertz-Fowler Paul Mooney Chris Peacock Adrian Tivey Valerie Wood Project Management Bart Barrell Julian Parkhill Marie-Adele Rajandream Al Ivens Neil Hall Matthew Berriman Stephen Bentley Nick Thomson Karen Mungall Ian Goodhead Zahra Hance Heidi Hauser Mandy Sanders Mark Simmonds Danielle Walker Sequencing Carol Churcher Karen Brooks Inna Cherevach Tracey Chillingworth Kay Clarke Paul Davis Nancy Hamlin Kay Jagels Sharon Moule Brian White Sally Whitehead Administration Yvonne Shaw Programming David Harper Rob Davies Arnaud Kerhornou Kim Rutherford Ed Zuiderwijk Subcloning Mike Quail Ann Cronin Claire Price Ester Rabbinowitsch Sarah Sharp Barbara Harris Becky Atkin Andrew Barron Louise Clarke Craig Corton Jonathan Doggett Nicola Lennard Alexandra Line Doug Ormond Analysis Ana Cerdeño-Tárraga Lisa Crossman Matthew Holden Keith James Arnab Pain Hubert Renauld Mohammed Sebaihia David Harris Matthew Collins Nigel Foster Arlette Goble Lee Murphy Susan O’Neil Simon Rutter David Saunders Kathy Seeger Robert Squares Steven Squares Mapping John Woodward Comparative Genomics Alison Dennis Emily Kay Helena Seth-Smith Pathogen Microarrays Gareth Bloomfield Celine Carret Theresa Fetwell Maria Fookes Nefeli Nikolaidou-Katsaridou Matloob Qureshi Jason Skelton Funding

13. Prokaryotic genomes

14. Eukaryotic genomes