Marie-Adèle Rajandream The Pathogen Sequencing Unit The Sanger Institute The Wellcome Trust Genome Campus Hinxton Cambridge United Kingdom

The Sanger Institute  Principally funded by Wellcome Trust (about 96 %)  60,000,000 bases per day of raw data  600 employees  Sequencing of Human, Mice, Zebrafish & pathogen genomes  Manual and automatic genome annotation (Ensembl, Artemis)  Identification of cancer causing mutations (recently BRAF gene mutation)  Sequence variation and disease association

Sequencing  Small genomes (bacterial and model organisms)  projects  Current capacity 4 M reads p/a sufficient for 100 Mb of finished sequence  Mainly whole genome/chromosome shotguns including finishing  Many are international collaborations  Larger more complex genomes ( Mb) on the horizon Informatics  Automatic analysis  Manual annotation by expert biologists  Tools: finishing (Cyclops), annotation (Artemis), comparative analysis (ACT)  Data dissemination  Database resources Functional Genomics  S. pombe  Bacterial Genomes  D. discoideum The Pathogen Sequencing Unit

GeneDB

Project pages annotation sequences analysis GeneDB FTP site BLAST curation

What is GeneDB? a generic organism database annotated sequences as well as functional data visualisation in user-friendly environment annotation and analysis of data by biologists flexible enough to incorporate new data types linked to external databases fully curated

The GeneDB project Started in 2001 Funded by the Wellcome Trust for a period of 5 years Initially for 3 organisms: S. pombe, Leishmania & Trypanosome 2 full-time programmers, 1 part-time programmer One curator for each organism One helpdesk person / programmer Prototype now done and in use

Technical Outline Prototype “Java” biojava data gui minelet mining test utils web Web jspcgi blast ominblast aspcommon cerevisiae pombe malaria leish tryp Data asp images serialise indices cerevisiae images serialise indices pombe malaria tryp leish EMBL

Broad specifications for production version Relational database Curator / annotator interface incorporating functionality of Artemis (MESS) Facility for doing more complex queries For comprehensive, detailed specs see our Functional Specifications document

P. falciparum chr. 14

“biotin carboxylase” Inferred by Sequence Similarity with a yeast sequence SGD:S (which was originally annotated based on a published mutant phenotype)

Pathogen Sequencing Unit Analysis Martin Aslett Steven Bentley Matthew Berriman Ana Cerdeno Christiane Hertz-Fowler Matthew Holden Keith James Rachel Lyne Arnab Pain Chris Peacock Mohammed Sebaihia Nick Thomson Valerie Wood Project Management Bart Barrell Julian Parkhill Marie-Adele Rajandream Al Ivens Neil Hall Programming Rob Davies David Harper Arnaud Kerhornou Paul Mooney Kim Rutherford Adrian Tivey Ed Zuiderwijk Karen Mungall Theresa Feltwell Ian Goodhead Zahra Hance Heidi Hauser Mandy Sanders Mark Simmonds Danielle Walker Barbara Harris Becky Atkin Andrew Barron Carol Chillingworth Louise Clarke Craig Corton Jonathan Doggett Nicola Lennard Alexandra Line Doug Ormand David Harris Matthew Collins Nigel Fosker Arlette Goble Lee Murphy Susan O’Neil Simon Rutter David Saunders Kathy Seeger Robert Squares Steven Squares Carol Churcher Karen Brooks Inna Cherevach Tracey Chillingworth Kay Clarke Paul Davies Nancy Hamlin Kay Jagels Sharon Moule Brian White Sally Whitehead Subcloning Ann Cronin Audrey Fraser David Johnson Mike Quail Claire Price Ester Rabbinowitsch Sarah Sharp Mapping Maria Fookes John Woodward Sequencing Wellcome Trust Sanger Institute Administration Yvonne Shaw