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OJBTM
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: cputonti@luc.edu
ABSTRACT
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): 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 www.bioinfo.uh.edu/csPCR.