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Online Journal of Bioinformatics  

 Volume 11 (1): 34-37, 2010

csPCR: A computational tool for the simulation of the Polymerase Chain Reaction.


Sandhya Dasu1, April Williams2,3, Yuriy Fofanov1,4 and Catherine Putonti2,3,4,5*


1Department(s) of Computer Science and 4Biology, University of Houston,  2Department(s) of Biology, 3Bioinformatics and 5Computer Science, Loyola University Chicago, USA *Corresponding Author:




Dasu S, Williams A, Fofanov Y, Putonti C., csPCR: A computational tool for the simulation of the Polymerase Chain Reaction, Onl J Bioinform., 11 (1): 34-37, 2010 Herein we present a computational simulation package PCR (csPCR) which models the PCR reaction, taking into consideration the issues of specificity, sensitivity, potential mishybridizations throughout the primer sequence as well as at the 3 end, and primer interactions, including self-complementarity and primer-primer interactions. A single target sequence or multiple target sequences can be considered simultaneously in addition to multiple primer sequences; thus a complex community and/or a multiplex assay can be simulated in a manner analogous with the actual experiment. This tool leaves primer design to the user, as there is a wealth of existing programs already available, and rather focuses on simulation of the anticipated amplification and expected agarose gel in addition to providing information about the location(s) of amplification in both text and graphical format. The software is freely available at