In partial fulfillment of the Requirements for the Degree of
Master of Science

Jing Liu
will defend her thesis

Design and Implementation of a Software Tool for Large Scale Primer Design

Selecting proper primers is one of the most important steps in designing the PCR (polymerase chain reaction) experiment. Due to the manual nature of current primer design programs, large-scale primer design remains impractical. This project concerns the implementation of a software tool to design primers over a large genome region for segments of DNA that have some given combination of biological features. This software retrieves the biological features from a database, performs the calculation to determine the candidate sequences, designs primers for each of these sequences, arranges PCR experiments into 96 well trays, and stores the results into database tables for future reference. The software is highly automated and supports fast computation of primers. It allows individual tailoring of primer selecting criteria, yet requires only a minimal set of user-defined parameters. It organizes the primers in the database tables in a bench-oriented way, and uniquely identifies each primer to avoid the cost of re-synthesizing existent primers. The software has been tested in the Human Genome Sequencing Center of the Baylor College of Medicine, yielding satisfactory results. With the advent of large-scale primer design software and oligo-nucleotides synthesis facilities, many new biology applications are possible.