Research Presentation
Nordborg LabUniversity of Southern California
Helly KweeAugust 21, 2003
Southern California Bioinformatics Summer Institute
Agenda
• Research area overview
• Projects
• Bioinformatics Tools
• Current State of Affairs
• Conclusion (Impacts)
Overview
• Genetic basis of adaptation
• Map loci conferring natural variation in Arabidopsis thaliana
• NSF 2010 Project
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
Bioinformatics Tools
• Revised database schema
• Populating the database
• Revised web-based viewers– Genome– Polymorphism– Alignment
Code Revision I
alignmentviewer.pldb.pm viewer.pm
alignmentviewer.pl
genomeviewer.pl
polymorphismviewer.pl
genomeviewer.pl
polymorphismviewer.pl
Modules
Screenshot-- Alignment Viewer
Screenshot– Genome ViewerScreenshot-- Genome Viewer
Screenshot-- Polymorphism Viewer
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
Questions
?
Acknowledgements
• Dr. Nordborg and his lab
• SoCalBSI faculty
• NSF and NIH