Supplementary Data for "TaqSim: TaqMan PCR Simulator"
Authors:
Matthew D. Dyer, Shea N. Gardner, Jason R. Smith, Beth Vitalis, Clinton Torres, Thomas A. Kuczmarski, and Thomas Slezak.Citation:
(In Review)Description:
Polymerase chain reaction (PCR) has become a key molecular biology tool with many applications. Although PCR techniques are simple and well defined, they can be time consuming as well as unpredictable in the case of degenerate primers or multiplex primer mixes where multiple reactions are tested simultaneously to reduce expenses. The unpredictability arises from the fact that the components of the individual primer sets may cross-react with each other, yielding unexpected and confusing results. In an effort to eliminate these problems and we have developed TaqSim, a perl program that simulates various types of PCR reactions.The advantage of TaqSim is that it is run from a
command-line and can generate output files in a
number of formats allowing it to serve as a front-end or
back-end for other software. Users can select between a
number of PCR applications including the traditional
forward/reverse primer pair (simple), inclusion of an
internal oligo (triplet), and multiplex reactions. TaqSim
allows users to define the search set so you can
easily search a single genome or all known sequences.
TaqSim allows users to adjust runtime settings like the
number of allowed mismatches, maximum amplicon length,
primer hybridization temperatures, and the allowance of
degenerate primers which allows the user to model their
specific experimental needs. If specified,
TaqSim partitions input data into subsets and runs them
each in parallel allowing users to make use of
multiprocessor machines and reduce running time.
Data:
| File | Description | Links |
|---|---|---|
| Software | TaqSim package. | .tar.gz
.zip |
| TaqSim help document. | ||
| Other
files |
TaqSim output for analysis of Multiplex Sinorhizobium meliloti experiment. | .xls |
| TaqSim output for intitial SARS analysis. | .xls | |
| TaqSim output for subsequent SARS analysis with added Bat SARS strains. | .xls |