November 2007 BRC5 Bethesda

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)