csPCR                 

ABSTRACT

Summary: Polymerase Chain Reaction or PCR-based methods are ubiquitous within the research laboratory and clinical molecular medicine, providing a rapid, sensitive means of detection and diagnosis.  Although there has been substantial experimental application of the PCR based technique, comprehensive computational simulations which incorporate many of the factors at play in real experiments have not been explored.  Herein we present a Windows-based application csPCR developed using the C# language. This application provides a graphical prediction of an agarose gel for any given sequence(s) and primer(s), and while considering possible non-specific binding as well as interactions between primers such as cross-hybridization. Applications include screen primers against the sequences of possible contaminants to ensure target specificity in addition to simulating non-specific hybridizations to compare with unexpected experimental amplification.

Availability and Implementation: www.bioinfo.uh.edu/csPCR

Contact: cputonti(AT)luc.edu

Click here to download zipped source code.

Click here to download user documentation.