Vector. Base Seth Redmond Imperial College, London seth. redmond@imperial. ac. uk Vector. Base
Vector. Base “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 Vector. Base
Aedes aegyptii (Yellow Fever) A. gambiae (PEST) (Malaria) Culex pipens (Filariasis) Pediculus humanus Ixodes Scapularis (Misc - body louse) (Lyme Disease) Lutzomyia longipalpis (Leishmaniasis) Glossina Morsitans Rhodnius prolixus (Sleeping sickness) (Chagas Disease) Phlebotomus papatasi (Leishmaniasis) Vector. Base A. gambiae (M) A. gambiae (S)
COMP ANNOT EST ANNOT MAN ANNOT PROBE ALIGNS HOSTING & INTEGRATION PROT ANNOT Vector. Base MAN ANNOT
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Vector. Base
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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. Ano. EST clusters • ‘Temporary’ servers • Preliminary data – e. g. array mappings between genebuilds • Collaborative use Vector. Base
Permanent Servers • A Gambiae – Manual annotation • Vector. Base manual • CEGG Immunity set – Comp annotation • Ano. EST Clusters • Re. Ano. CDS – Transposons Vector. Base • A. Aegypti – Comp Annotation • Aed. EST Clusters
LO OL AP CE GG Vector. Base
LO OL AP CE GG Vector. Base
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DAS requests… • Versioning – Old features / New assemblies • Nested Features – Sim to GFF 3, refer to parent ID to allow construction of gene models Vector. Base
• 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 Vector. Base
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