![Page 1: Research Presentation Nordborg Lab University of Southern California](https://reader036.vdocuments.us/reader036/viewer/2022062322/568144ab550346895db17265/html5/thumbnails/1.jpg)
Research Presentation
Nordborg LabUniversity of Southern California
Helly KweeAugust 21, 2003
Southern California Bioinformatics Summer Institute
![Page 2: Research Presentation Nordborg Lab University of Southern California](https://reader036.vdocuments.us/reader036/viewer/2022062322/568144ab550346895db17265/html5/thumbnails/2.jpg)
Agenda
• Research area overview
• Projects
• Bioinformatics Tools
• Current State of Affairs
• Conclusion (Impacts)
![Page 3: Research Presentation Nordborg Lab University of Southern California](https://reader036.vdocuments.us/reader036/viewer/2022062322/568144ab550346895db17265/html5/thumbnails/3.jpg)
Overview
• Genetic basis of adaptation
• Map loci conferring natural variation in Arabidopsis thaliana
• NSF 2010 Project
![Page 4: Research Presentation Nordborg Lab University of Southern California](https://reader036.vdocuments.us/reader036/viewer/2022062322/568144ab550346895db17265/html5/thumbnails/4.jpg)
![Page 5: Research Presentation Nordborg Lab University of Southern California](https://reader036.vdocuments.us/reader036/viewer/2022062322/568144ab550346895db17265/html5/thumbnails/5.jpg)
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
![Page 6: Research Presentation Nordborg Lab University of Southern California](https://reader036.vdocuments.us/reader036/viewer/2022062322/568144ab550346895db17265/html5/thumbnails/6.jpg)
Bioinformatics Tools
• Revised database schema
• Populating the database
• Revised web-based viewers– Genome– Polymorphism– Alignment
![Page 7: Research Presentation Nordborg Lab University of Southern California](https://reader036.vdocuments.us/reader036/viewer/2022062322/568144ab550346895db17265/html5/thumbnails/7.jpg)
Code Revision I
alignmentviewer.pldb.pm viewer.pm
alignmentviewer.pl
genomeviewer.pl
polymorphismviewer.pl
genomeviewer.pl
polymorphismviewer.pl
Modules
![Page 8: Research Presentation Nordborg Lab University of Southern California](https://reader036.vdocuments.us/reader036/viewer/2022062322/568144ab550346895db17265/html5/thumbnails/8.jpg)
Screenshot-- Alignment Viewer
![Page 9: Research Presentation Nordborg Lab University of Southern California](https://reader036.vdocuments.us/reader036/viewer/2022062322/568144ab550346895db17265/html5/thumbnails/9.jpg)
Screenshot– Genome ViewerScreenshot-- Genome Viewer
![Page 10: Research Presentation Nordborg Lab University of Southern California](https://reader036.vdocuments.us/reader036/viewer/2022062322/568144ab550346895db17265/html5/thumbnails/10.jpg)
Screenshot-- Polymorphism Viewer
![Page 11: Research Presentation Nordborg Lab University of Southern California](https://reader036.vdocuments.us/reader036/viewer/2022062322/568144ab550346895db17265/html5/thumbnails/11.jpg)
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
![Page 12: Research Presentation Nordborg Lab University of Southern California](https://reader036.vdocuments.us/reader036/viewer/2022062322/568144ab550346895db17265/html5/thumbnails/12.jpg)
Questions
?
![Page 13: Research Presentation Nordborg Lab University of Southern California](https://reader036.vdocuments.us/reader036/viewer/2022062322/568144ab550346895db17265/html5/thumbnails/13.jpg)
Acknowledgements
• Dr. Nordborg and his lab
• SoCalBSI faculty
• NSF and NIH