GeneDB: A database for Prokaryotic and

Eukaryotic Organisms

Pathogen Sequencing Unit

The Wellcome Trust Sanger Institute

Pathogen Sequencing Unit(http://www.sanger.ac.uk/Projects/)

Bacteria:M. tuberculosisM. lepraeY. pestisS. typhiC. diphtheriaB. pseudomallei

Yeasts and Fungi:Schizosaccharomyces pombeAspergillus fumigatusPneumocystis carinii

Protozoa:Plasmodium falciparumLeishmaniaTrypanosomaEimeriaTheileria

The Pathogen Group is funded to sequence the genomes of a wide range of prokaryotic and eukaryotic organisms

Dissemination of informationsequence and annotation

Sequence databases(EMBL, Genbank, Swiss-Prot)

Sanger Institute Project pages

BLAST

FTP site

Analysis

GeneDB

GeneDB mining code

links to feature pages

GeneDBserialisedobjectstools

reports flatfiles

GUS

Java Servlets/JSP classes

ftp

BLAST

EMOWSE Motif search

sequenceannotation

curation

cross-references

validation 10 sequencedatabases

Curated proteindatabases

Functional genomicsresources

Protein domaindatabases

value addition

submissions/updates

Organism databases

GeneOntology

Protein motif predictions

Gene prediction tools

Database searches

User data submissions and updates

Literature searches

a) Basic information

b) Location

c) Curated annotation

d) Predicted peptide properties

e) Gene Ontology: annotationusing the GO controlled vocabulary

g) Curated orthologs

h) Similarity information

i) Swiss-Prot annotations

j) Contact details

f) Database cross references

Curation within GeneDB

• 1 curator per organism/related species

• maintenance of sequence data / annotationof multi-centre of often unfinished projects

• integration of information extracted from literature, public databases, communityfeedback using structured syntax/vocabulary

• nomenclature

(PMID:12574127)

AnalysisAna Cerdeño-TárragaLisa CrossmanMatthew HoldenKeith James Arnab PainHubert RenauldMohammed Sebaihia

Project ManagementBart BarrellJulian ParkhillMarie-Adele RajandreamAl IvensNeil Hall Matthew BerrimanStephen Bentley Nick Thomson Programming

David HarperRob DaviesArnaud KerhornouKim RutherfordEd Zuiderwijk

Karen MungallIan GoodheadZahra HanceHeidi HauserMandy SandersMark SimmondsDanielle Walker

Barbara HarrisBecky AtkinAndrew BarronLouise ClarkeCraig CortonJonathan DoggettNicola LennardAlexandra LineDoug Ormond

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

Carol ChurcherKaren Brooks Inna CherevachTracey ChillingworthKay ClarkePaul DavisNancy HamlinKay JagelsSharon MouleBrian WhiteSally Whitehead

SubcloningMike QuailAnn Cronin Claire Price Ester Rabbinowitsch Sarah Sharp

AdministrationYvonne Shaw

MappingJohn Woodward

Sequencing

Funding

Pathogen MicroarraysGareth BloomfieldCeline CarretTheresa FetwellMaria Fookes Nefeli Nikolaidou-KatsaridouMatloob QureshiJason Skelton

DatabasesMartin AslettAndy BerryChristiane Hertz-FowlerPaul MooneyChris PeacockAdrian TiveyValerie Wood

Comparative GenomicsAlison DennisEmily KayHelena Seth-Smith

Prokaryotic genomesBacteriovorax marinus Bacterial parasite In progress Bacteroides fragilis (x2) Opportunistic Complete Bordetellae (x3) Whooping cough Published Burkholderia cenocepacia (B. cepacia) Lung infections in CF Complete

Burkholderia pseudomallei Melioidosis Complete

Campylobacter jejuni Food poisoning Published

Chlamidia trachomatis Tracoma Funded

Chlamidophila abortus Veterinary Complete Citrobacter rodentium Mouse enteropathogen In progress Clavibacter michiganensis Plant pathogen In progress Clostridium botulinum Botulism Complete Clostridium difficile Colitis Complete Corynebacterium diphtheriae Diphtheria Publication in press Cowdria rumiantium Heartwater/Cowdriosis In progress Erwinia carotovora Plant pathogen Complete Escherichia/Shigella spp. (x5) Various In progress Helicobacter mustelae Veterinary Funded Mycobacterium bovis Veterinary/Tuberculosis Published Mycobacterium leprae Lepra Published Mycobacterium marinum Various In progress Mycobacterium tuberculosis Tuberculosis Published Neisseria lactamica Human comensal Funded Neisseria meningitidis (serogroup A) Bacterial meningitis Published Neisseria meningitidis (serogroup C) Bacterial meningitis Complete Photorhabdus asymbiotica Opportunistic In progress Proteus mirabilis Urinary infections Funded Pseudomonas fluorescens Plant saprophyte In progress Rhizobium leguminosarum Plant symbiont In progress Salmonella spp. (x5) Various In progress Salmonella typhi Typhoid fever Published Serratia marcescens Opportunistic In progress Staphylococcus aureus (MRSA) Various (Nosocomial) Complete Staphylococcus aureus (MSSA) Various (Community acquired) Complete Stenotrophomonas maltiphilia Bacteraemia Funded Streptococcus equi Veterinary In progress Streptococcus pneumoniae Bacterial meningitis Complete Streptococcus pyogenes Various (ARF-associated) Complete Streptococcus suis Veterinary In progress Streptococcus uberis Veterinary In progress Streptomyces coelicolor Model organism Published Tropheryma whipleii Whipple’s disease Published Wolbachia (Culex quinquefasciatus) Vector (Bancroftian filariasis) Approved Wolbachia (Onchocerca volvulus) River Blindness Funded Yersinia pestis Black death Published Yersinia enterocolitica Food poisoning Complete

Eukaryotic genomes

Schizosaccharomyces pombe Published Saccharimyces cerevisiae Published Plasmodium falciparum Malaria Published Plasmodium chabaudi Partial shotgun Plasmodium berghei Partial shotgun Plasmodium gallinaceum Whole shotgun Plasmodium knowlesi Partial shotgun Leishmania major Leishmaniasis Complete/ In progress Chs 1, 3 Published (Seattle) Chrs 4-26 Complete/ In progress Chr 28 In progress Chrs 30-34 Complete/ In progress Chr 36 In progress Trypanosoma brucei African trypanosomiasis Chrs I-II Published (TIGR) Chrs IX, X, XI In progress Trypanosoma congolense Veterinary trypanosomiasis In progress/Partial shotgun Trypanosoma vivax Veterinary trypanosomiasis In progress/Partial shotgun Eimeria tenella Coccidiosis Partial shotgun Dictyostelium discideum Model organism Chr 6 In progress Chr 5 In progress Babesia bovis - EST Veterinary In progress Theileria annulata Veterinary Whole shotgun Toxoplasma gondonii Toxoplasmosis Whole shotgun Entamoeba histolytica Amoebic dysentery Whole shotgun Entamoeba dispar Non-pathogenic E. histolytica Genome survey Entamoeba invadens Similar to amoebic dysentery Genome survey Entamoeba moshkovskii Free-living amoeba Genome survey Entamoeba terrapinae Veterinary Genome survey Aspergillus fumigatus Fungi In progress Pneumocystis carinii Infection immunocompromised In progress Brugia malaii Parasite nematode In progress Glossina morsitans - EST Parasite vector Publication submitted