November 2007BRC5 Bethesda Variation data in VectorBase Dan Lawson, VectorBase EMBL-EBI.

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Presentation transcript:

November 2007BRC5 Bethesda Variation data in VectorBase Dan Lawson, VectorBase EMBL-EBI

November 2007BRC5 Bethesda 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

November 2007BRC5 Bethesda Showing SNPs in ContigView

November 2007BRC5 Bethesda Showing SNPs in ContigView

November 2007BRC5 Bethesda SNP Report

November 2007BRC5 Bethesda SNP Report - SNP context

November 2007BRC5 Bethesda TranscriptSNPview

November 2007BRC5 Bethesda

November 2007BRC5 Bethesda GeneSNPview

November 2007BRC5 Bethesda Navigation through SNP pages

November 2007BRC5 Bethesda

November 2007BRC5 Bethesda

November 2007BRC5 Bethesda Alignment of strain sequences

November 2007BRC5 Bethesda Tabulated SNP details

November 2007BRC5 Bethesda 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

November 2007BRC5 Bethesda SNP calling in A. gambiae S form » Data from Ewen Kirkness (JCVI) » 2.1 million potential SNPs

November 2007BRC5 Bethesda 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)