Transcript Variation data in VectorBase

Variation data in VectorBase
Dan Lawson,
VectorBase EMBL-EBI
November 2007
BRC5 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 2007
BRC5 Bethesda
Showing SNPs in ContigView
November 2007
BRC5 Bethesda
Showing SNPs in ContigView
November 2007
BRC5 Bethesda
SNP Report
November 2007
BRC5 Bethesda
SNP Report - SNP context
November 2007
BRC5 Bethesda
TranscriptSNPview
November 2007
BRC5 Bethesda
November 2007
BRC5 Bethesda
GeneSNPview
November 2007
BRC5 Bethesda
Navigation through SNP pages
November 2007
BRC5 Bethesda
November 2007
BRC5 Bethesda
November 2007
BRC5 Bethesda
Alignment of strain sequences
November 2007
BRC5 Bethesda
Tabulated SNP details
November 2007
BRC5 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 2007
BRC5 Bethesda
SNP calling in A. gambiae S form
» Data from Ewen Kirkness (JCVI)
» 2.1 million potential SNPs
November 2007
BRC5 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)
November 2007
BRC5 Bethesda