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Variation data in VectorBase

Variation data in VectorBase. Dan Lawson, VectorBase EMBL-EBI. Variation database. Use Ensembl Variation database schema Ancilliary database to ‘core’ Perl API for programmatic access Biomart implementation for data mining Align reads to reference genome and call SNPs.

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Variation data in VectorBase

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  1. Variation data in VectorBase Dan Lawson, VectorBase EMBL-EBI BRC5 Bethesda

  2. Variation database • Use Ensembl Variation database schema • Ancilliary database to ‘core’ • Perl API for programmatic access • Biomart implementation for data mining • Align reads to reference genome and call SNPs BRC5 Bethesda

  3. Showing SNPs in ContigView BRC5 Bethesda

  4. Showing SNPs in ContigView BRC5 Bethesda

  5. SNP Report BRC5 Bethesda

  6. SNP Report - SNP context BRC5 Bethesda

  7. TranscriptSNPview BRC5 Bethesda

  8. BRC5 Bethesda

  9. GeneSNPview BRC5 Bethesda

  10. Navigation through SNP pages BRC5 Bethesda

  11. BRC5 Bethesda

  12. BRC5 Bethesda

  13. Alignment of strain sequences BRC5 Bethesda

  14. Tabulated SNP details BRC5 Bethesda

  15. More Anopheles gambiae genomes • Sequencing of A. gambiae M & S forms complete • M form (WashU GSC) 2,754,999 reads • S form (JCVI) 2,714,217 reads • Planned sequencing for 12 genome Anopheles cluster BRC5 Bethesda

  16. SNP calling in A. gambiae S form • Data from Ewen Kirkness (JCVI) • 2.1 million potential SNPs BRC5 Bethesda

  17. Summary • (Re)-use of well established data structure • Extensive set of visualization tools • Data mining via BioMart tool • Programmatic access through Ensembl • Ability to handle re-sequencing data (including new technologies) BRC5 Bethesda

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