1. Research Presentation Nordborg Lab University of Southern California Helly Kwee August 21, 2003 Southern California Bioinformatics Summer Institute

2. Agenda Research area overview Projects Bioinformatics Tools Current State of Affairs Conclusion (Impacts)

3. Overview Genetic basis of adaptation Map loci conferring natural variation in Arabidopsis thaliana NSF 2010 Project

5. Projects Genomic survey of polymorphism in A. thaliana – Sequence ~2000 fragments from 96 accessions – Phenotype various traits – Association analysis Bioinformatics tools: – Publicly accessible database – Web-based viewers

6. Bioinformatics Tools Revised database schema Populating the database Revised web-based viewers – Genome – Polymorphism – Alignment

7. Database Contents

8. Code Revision I alignmentviewer.pl db.pm viewer.pm alignmentviewer.pl genomeviewer.pl polymorphismviewer.pl genomeviewer.pl polymorphismviewer. pl Module s

9. Screenshot-- Alignment Viewer

10. Screenshot– Genome Viewer Screenshot-- Genome Viewer

11. Screenshot-- Polymorphism Viewer

12. Impacts Insights into genetic basis of natural variation Genes responsible for agriculturally important traits Tools and methods --> applicable to economically important organisms Database as training tool

13. Questions ?

14. Acknowledgements Dr. Nordborg and his lab SoCalBSI faculty NSF and NIH