Variation data in Vector Base Dan Lawson Vector
Variation data in Vector. Base Dan Lawson, Vector. Base EMBL-EBI November 2007 BRC 5 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 BRC 5 Bethesda
Showing SNPs in Contig. View November 2007 BRC 5 Bethesda
Showing SNPs in Contig. View November 2007 BRC 5 Bethesda
SNP Report November 2007 BRC 5 Bethesda
SNP Report - SNP context November 2007 BRC 5 Bethesda
Transcript. SNPview November 2007 BRC 5 Bethesda
November 2007 BRC 5 Bethesda
Gene. SNPview November 2007 BRC 5 Bethesda
Navigation through SNP pages November 2007 BRC 5 Bethesda
November 2007 BRC 5 Bethesda
November 2007 BRC 5 Bethesda
Alignment of strain sequences November 2007 BRC 5 Bethesda
Tabulated SNP details November 2007 BRC 5 Bethesda
More Anopheles gambiae genomes » Sequencing of A. gambiae M & S forms complete » M form (Wash. U GSC) 2, 754, 999 reads » S form (JCVI) 2, 714, 217 reads » Planned sequencing for 12 genome Anopheles cluster November 2007 BRC 5 Bethesda
SNP calling in A. gambiae S form » Data from Ewen Kirkness (JCVI) » 2. 1 million potential SNPs November 2007 BRC 5 Bethesda
Summary » (Re)-use of well established data structure » Extensive set of visualization tools » Data mining via Bio. Mart tool » Programmatic access through Ensembl » Ability to handle re-sequencing data (including new technologies) November 2007 BRC 5 Bethesda
- Slides: 17