vectorbase seth redmond imperial college, london [email protected]
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VectorBaseVectorBase
VectorBase“A Relational Bioinformatics Resource Center for
Arthropod Vectors of Human pathogens”
• Funded by NIAID (National Institute of Allergy & Infectious Diseases - US)
• One of a set of BRC’s funded to support large-scale sequencing projects
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Aedes aegyptii
(Yellow Fever)
A.gambiae (PEST)
(Malaria)
A.gambiae (M) A.gambiae (S)
Culex pipens
(Filariasis)
Pediculus humanus
(Misc - body louse)
Ixodes Scapularis
(Lyme Disease)
Lutzomyia longipalpis
(Leishmaniasis)
Glossina Morsitans
(Sleeping sickness)
Rhodnius prolixus
(Chagas Disease)
Phlebotomus papatasi
(Leishmaniasis)
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PROBEALIGNS
COMPANNOT
MANANNOT
ESTANNOT
MANANNOT
PROTANNOT
HOSTING &INTEGRATION
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APOLLO
DAS
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DASserver
DAS
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DAS
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DASclient
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VB DAS use• e! DAS client• Permanent DAS servers:
• Rapidly changing features– e.g. manual annotation
• Low priority / low usage features– e.g. AnoEST clusters
• ‘Temporary’ servers• Preliminary data
– e.g. array mappings between genebuilds
• Collaborative use
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Permanent Servers
• A Gambiae– Manual annotation
• VectorBase manual• CEGG Immunity set
– Comp annotation• AnoEST Clusters• ReAnoCDS
– Transposons
• A.Aegypti– Comp Annotation
• AedEST Clusters
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DAS
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DAS requests…
• Versioning– Old features / New assemblies
• Nested Features– Sim to GFF3, refer to parent ID to allow
construction of gene models
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• Imperial– Fotis Kafatos
– George Christophides
– Bob Maccallum
• EBI– Ewan Birney
– Dan Lawson
– Martin Hammond
– Karyn Megy
• Harvard– William Gelbart
– Susan Russo
– Kathy Campbell
• Notre Dame– Frank Collins
– Rob Bruggner
– EO. Stinson
– Neil Lobo
• IMBB– Kitsos Louis
– Pantelis Topalis