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csPCR: A computational tool for the simulation of the Polymerase Chain Reaction
Online Journal of Bioinformatics
  • Sandhya Dasu
  • April Williams
  • Yuriy Fofanov, University of Texas Medical Branch
  • Catherine Putonti, Loyola University Chicago
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Online Journal of Bioinformatics
Dasu S, Williams A, Fofanov Y, Putonti C., csPCR: A computational tool for the simulation of the Polymerase Chain Reaction, Online J Bioinformatics, 11 (1): 30-33, 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 selfcomplementarity 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

Author Posting. © Online Journal of Bioinformatics, 2010. This article is posted here by permission of the OJB for personal use, not for redistribution. The article was published in the Online Journal of Bioinformatics, Volume 11, Issue 1, 2012.

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Creative Commons Attribution-Noncommercial-No Derivative Works 3.0
Citation Information
Sandhya Dasu, April Williams, Yuriy Fofanov and Catherine Putonti. "csPCR: A computational tool for the simulation of the Polymerase Chain Reaction" Online Journal of Bioinformatics Vol. 11 Iss. 1 (2010)
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