Gne-primer : a PCR primer design program

• Main Author: Kok, Wui Lim.
• Other Authors: Kwoh, Chee Keong
• Format: Theses and Dissertations
• Published: 2008
• Subjects: DRNTU::Engineering::Computer science and engineering::Computer applications::Life and medical sciences
• Online Access: http://hdl.handle.net/10356/2675
• Institution: Nanyang Technological University

Proper PCR primer design determines the success or failure of Polymerase Chain Reaction (PCR) reactions. In this project, we develop GENE-PRIMER, a genome- specific PCR primer design program that is amenable to a genome-wide scale. To achieve this, we incorporated various parameters with biological significance into our program, namely, primer length, melting temperature of primers Tm, guanine/cytosine (GC) content of primer, homopolymeric runs in primer and self- hybridization tendency of primer. In addition, BLAST algorithm is utilized for the purpose of primer specificity check. In summary, selected primers adhered to both physico-chemical criteria and also display specificity to intended binding site in the genome.