Marie-Adèle RajandreamThe Pathogen Sequencing Unit

The Sanger InstituteThe Wellcome Trust Genome Campus

HinxtonCambridge

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) 60-70 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 (35-100 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

http://www.genedb.org

Project pages

annotation

sequencesanalysis

GeneDBhttp://www.genedb.org

FTP site

BLASTcuration

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

jsp cgi

blast

ominblast

asp common

cerevisiae

pombe

malaria

leish

tryp

Data

aspimagesserialiseindices

cerevisiaeimagesserialiseindices

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 sequenceSGD:S0005299

(which was originally annotated based on a published

mutant phenotype)

Pathogen Sequencing Unit

AnalysisMartin AslettSteven Bentley Matthew BerrimanAna CerdenoChristiane Hertz-FowlerMatthew HoldenKeith JamesRachel Lyne Arnab PainChris PeacockMohammed Sebaihia Nick Thomson Valerie Wood

Project ManagementBart BarrellJulian ParkhillMarie-Adele RajandreamAl IvensNeil Hall

ProgrammingRob DaviesDavid HarperArnaud KerhornouPaul MooneyKim RutherfordAdrian TiveyEd Zuiderwijk

Karen MungallTheresa FeltwellIan GoodheadZahra HanceHeidi HauserMandy SandersMark SimmondsDanielle Walker

Barbara HarrisBecky AtkinAndrew BarronCarol ChillingworthLouise ClarkeCraig CortonJonathan DoggettNicola LennardAlexandra LineDoug Ormand

David HarrisMatthew CollinsNigel FoskerArlette GobleLee MurphySusan O’NeilSimon RutterDavid SaundersKathy SeegerRobert SquaresSteven Squares

Carol ChurcherKaren Brooks Inna CherevachTracey ChillingworthKay ClarkePaul DaviesNancy HamlinKay JagelsSharon MouleBrian WhiteSally WhiteheadSubcloning

Ann CroninAudrey FraserDavid JohnsonMike QuailClaire Price Ester Rabbinowitsch Sarah Sharp

MappingMaria FookesJohn Woodward

Sequencing

Wellcome Trust Sanger Institute

AdministrationYvonne Shaw