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New Genomes

New Genomes. Dan Lawson. White papers. NHGRI White papers. Others. Sandflies Lutzomyia longipalpis Phlebotomus papatasi. Anopheles (AGCC) Anopheles arabiensis Anopheles quadriannulatus Anopheles merus Anopheles melas Anopheles christyl Anopheles epiroticus Anopheles stephensi

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New Genomes

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  1. New Genomes Dan Lawson

  2. White papers NHGRI White papers Others Sandflies Lutzomyia longipalpis Phlebotomus papatasi Anopheles (AGCC) Anopheles arabiensis Anopheles quadriannulatus Anopheles merus Anopheles melas Anopheles christyl Anopheles epiroticus Anopheles stephensi Anopheles maculatus Anopheles funestus Anopheles minimus Anopheles culicifacies Anopheles farauti Anopheles dirus Anopheles atroparvus Anopheles albimanus Simulium Simulium vittatum Simulium sirbanum Simulium damnosum Simulium ochraceum Simulium squamosum Simulium thyolense Simulium santipauli Simulium woodi Simulium exiguum Simulium yahense Anopheles Anopheles darlingi* Anopheles stephensi Aedes Aedes albopictus Glossina Glossina palpalis Glossina fuscipes Glossina pallidipes Glossina brevipalpis Glossina austeni Stomoxys calcitrans Musca domestica i5K initiative ? Tick & Mites Leptotrombidium deliense Ixodes scapularis* Dermacentor variabilis Ornithodorus turicata VectorBase 2012 2

  3. Goals • To review the current and future genomes for which VectorBase expects to have some participation in the analysis and data dissemination. • To define policy on how many levels of support and give guidance as to expectations from VectorBase in each case. VectorBase 2012 3

  4. VectorBase role in genome projects • Tiers of support for genomes • Define at least 3 levels of VectorBase participation in genome projects • Full - VectorBase plays an active role in the primary annotation of the genome. In most cases we would be either the sole participant or provide coordination to the effort. • Partial - VectorBase plays an supportive role in the primary annotation of the genome. Integration of data is via direct collaboration with the sequencers and annotation group. • Portal - VectorBase will build a core database and resource from INSDC submission or AGP/GFF3 provider by a 3rd party website. Only requires loose collaboration with sequencers/annotation group. • No genome - No genome assembly is available (or forthcoming), VectorBase to host transcriptome assembly via GDAV. VectorBase 2012 4

  5. Stakeholders • VectorBase • Sequencing group • Annotation group • INSDC (GenBank/ENA) • 2nd databases (UniProt/RefSeq) VectorBase 2012 5

  6. Expectations (for the community) • Pre-site for early release • Integration as a core database • Inclusion in compara • Blast-able datasets • BioMart datasets • Downloads • assembly agp • scaffolds • contigs • cDNA peptide • GFF3 • GTF VectorBase 2012 6

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