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GeneDB: A database for Prokaryotic and Eukaryotic Organisms

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GeneDB: A database for Prokaryotic and Eukaryotic Organisms Pathogen Sequencing Unit The Wellcome Trust Sanger Institute – PowerPoint PPT presentation

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Title: 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 Trypano
soma Eimeria Theileria
3
Dissemination of information
sequence and annotation
4
GeneDB (http//www.genedb.org/)
  • houses data from finished and ongoing
  • prokaryotic and eukaryotic genome projects
  • provides an intuitive user interface, allowing
  • rapid data access and visualisation
  • integrates sequence and annotation with
  • diverse biological datasets

5
sequence annotation curation
GeneDB mining code
6
(No Transcript)
7
  • Basic information
  1. Location

c) Curated annotation
  1. Predicted peptide properties

8
  • Gene Ontology annotation
  • using the GO controlled vocabulary
  1. Curated orthologs
  1. Similarity information
  1. Swiss-Prot annotations
  1. Contact details

9
  • 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
(No Transcript)
11
(PMID12574127)
12
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 ONeil 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
(No Transcript)
14
Prokaryotic genomes




15
Eukaryotic genomes



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