research presentation nordborg lab university of southern california helly kwee august 21, 2003...

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