create.primers.tree: Tree-based Initialization of Primers.

In matdoering/openPrimeR: Multiplex PCR Primer Design and Analysis

Tree-based Initialization of Primers.

Description

Creates a set of candidate primers using a tree-based algorithm.

Usage

create.primers.tree(
  seqs,
  seq.IDs,
  seq.groups,
  start,
  end,
  primer.lengths,
  allowed.region.definition,
  max.degen,
  conservation,
  sample = "",
  identifier = "",
  updateProgress = NULL
)

Arguments

seqs	Template sequences.
seq.IDs	Identifiers of template sequences.
seq.groups	Group identifiers of template sequences.
start	For each template the start of the interval where primers should be created.
end	For each template the end of the interval where primers should be created.
primer.lengths	Vector of desired primer lengths.
allowed.region.definition	Definition of allowed regions.
max.degen	Maximal degeneracy of primers.
conservation	Required conservation of template regions considered for the generation of primers. Conservation identifies the top conserved percentile of possible primers.
sample	Sample name for the analysis.
identifier	Identifier (e.g. for directionality).
updateProgress	Shiny progress object.

Details

First, primers are aligned and their sequence similarity is determined to compute a phylogenetic tree using hierarchical clustering. Next, the tree is traversed from leaves to top in order to identify groups of primers that can be merged (consensus) without exceeding the maximum degeneracy of primers.

Value

A vector with initialized primers.

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