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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, 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 www.bioinfo.uh.edu/csPCR.
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