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

November 2007 BRC5 Bethesda

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


Showing SNPs in ContigView


SNP Report


SNP Report - SNP context


TranscriptSNPview


GeneSNPview


Navigation through SNP pages


Alignment of strain sequences


Tabulated SNP details


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


SNP calling in A. gambiae S form

» Data from Ewen Kirkness (JCVI)

» 2.1 million potential SNPs


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

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