research presentation nordborg lab university of southern california
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Research Presentation Nordborg Lab University of Southern California. Helly Kwee August 21, 2003 Southern California Bioinformatics Summer Institute. Agenda. Research area overview Projects Bioinformatics Tools Current State of Affairs Conclusion (Impacts). Overview. - PowerPoint PPT PresentationTRANSCRIPT
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