compute.Tm.sets: Cross-Dimerization Filtering

In matdoering/openPrimeR: Multiplex PCR Primer Design and Analysis

Cross-Dimerization Filtering

Description

Removes cross-dimerizing primers from the input data.

Usage

compute.Tm.sets(
  primer.df,
  template.df,
  Tm.brackets,
  settings,
  mode.directionality = c("fw", "rev"),
  primer_conc,
  template_conc,
  na_salt_conc,
  mg_salt_conc,
  k_salt_conc,
  tris_salt_conc,
  allowed.mismatches,
  allowed.other.binding.ratio,
  allowed.stop.codons,
  allowed.region.definition,
  disallowed.mismatch.pos,
  opti.mode = FALSE,
  required.cvg = NULL,
  primers.fw = NULL,
  diagnostic.location = NULL,
  updateProgress = NULL
)

Arguments

primer.df	Primer data frame.
template.df	Template data frame.
Tm.brackets	Data frame with target primer melting temperatures.
settings	A DesignSettings object.
mode.directionality	Identifier of strand for which primers shall be designed.
primer_conc	Primer concentration.
template_conc	Template concentration.
na_salt_conc	Sodium ion concentration.
mg_salt_conc	Magensium ion concentration.
k_salt_conc	Potassium ion concentration.
tris_salt_conc	Tris ion concentration.
allowed.mismatches	The number of mismatches primers are allowed to have with the templates.
allowed.other.binding.ratio	Ratio of primers allowed to bind to non-target regions.
allowed.stop.codons	Consider mismatch binding events that induce stop codons.
allowed.region.definition	Definition of the allowed region.
disallowed.mismatch.pos	The number of positions from the primer 3' end where mismatches should not be allowed. All primers binding templates with mismatches within disallowed.mismatch.pos from the 3' end are disregarded.
opti.mode	Compute optimization constraints and relax delta Tm if necessary.
required.cvg	Target coverage ratio.
primers.fw	Already designed primer sets for the target temperatures given in Tm.brackets. Used to determine cross-dimerization.
diagnostic.location	Directory for storing results.
updateProgress	Shiny progress callback function.
primers.rev	The primer data set to be filtered for cross-dimers.
opti.constraints	List with optimization constraint settings.
annealing.temp	The PCR annealing temperature.

Value

primers.rev with removed cross-dimerizing primers.

Primer data frames for every target temperature.

matdoering/openPrimeR documentation built on July 4, 2025, 3:59 a.m.