optimize.ILP: Solver for ILP Set Cover

In matdoering/openPrimeR: Multiplex PCR Primer Design and Analysis

Solver for ILP Set Cover

Description

Solves the primer set cover problem using an ILP formulation.

Usage

optimize.ILP(
  primer.df,
  template.df,
  settings,
  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,
  target.temps,
  required.cvg,
  fw.primers = NULL,
  diagnostic.location = NULL,
  timeout = Inf,
  updateProgress = NULL
)

Arguments

primer.df	Primer data frame to be optimized.
template.df	Template data frame with sequences.
settings	A DesignSettings object.
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 target binding sites used for evaluating the coverage. If allowed.region.definition is within, primers have to lie within the allowed binding region. If allowed.region.definition is any, primers have to overlap with the allowed binding region. The default is that primers have to bind within the target binding 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.
target.temps	Target melting temperatures for primer sets in Celsius.
required.cvg	Target coverage ratio of the templates by the primers.
fw.primers	List with optimized primer data frames corresponding to target.temps. Only required for optimizing both strand directions and only in the second optimization run in order to check for cross dimerization.
diagnostic.location	Directory for storing results.
timeout	Timeout in seconds for the optimization with ILPs.
updateProgress	Shiny progress callback function.

Value

List with optimization results.

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