University of Houston

Department of Computer Science

In Partial Fulfillment of the Requirements for the Degree of
Master of Science

Sandhya Dasu

Will defend her thesis

An Application for the Simulation of the Polymerase Chain Reaction for Organism Identification

Abstract

Rapid identification of organisms in a sensitive, reliable, and reproducible manner is critical for clinical diagnosis as well as detection of harmful contaminants. Polymerase Chain Reaction or PCR-based methods are the most widely used molecular test for organism identification, since these methods are easy to use and economical. Through PCR-based assays, an organism can be identified by its fingerprint, or the set of amplified regions produced during the experiment. This can be visualized by a variety of means including agarose gel electrophoresis in which the amplified sequences form measurable bands. Reproducibility of such a fingerprint is mandatory in order for future assays to conclusively determine the organism present in an unknown sample.

The ability to simulate PCR and visualize expected gel results can greatly help, not only in prediction, but also in identifying issues prior to an experimental investigation. For this reason, a Windows-based application has been developed using the C# language to simulate PCR-based fingerprinting. This application provides a graphical prediction of an agarose gel for any given sequence(s), primer(s), and experimental conditions while considering possible non-specific binding as well as interactions between primers such as cross-hybridization. Although the time taken for execution is proportional to the length of the DNA, the application can consider genomes in seconds for microbial analysis and in just a few minutes for eukaryotes.

Date: Wednesday, November 1, 2006
Time: 10:00 AM
Place: 550-PGH

Faculty, students, and the general public are invited.
Advisor: Dr. Yuriy Fofanov