select.primer.region.by.conservation: Selection by Conservation

In matdoering/openPrimeR: Multiplex PCR Primer Design and Analysis

Selection by Conservation

Description

Selects primer regions for initialization of primers according to their conservation scores.

Usage

select.primer.region.by.conservation(
  primer.range,
  ali.entropy,
  conservation,
  bin,
  gap.char = "-"
)

Arguments

primer.range	Data frame with primer starts/stops.
ali.entropy	Entropy values for the alignment.
conservation	Desired ratio of primer conservation. Only regions with a conservation of at least conservation are considered for the initialization of primers.
bin	DNABin alignment of templates.
gap.char	The character for alignment gaps.

Details

The conservation scores are computed using the entropies computed from the alignment of the template sequence regions of interests.

Value

Updated primer regions according to the desired conservation.

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