check_restriction_sites_single: Identification of Sequence Restriction Sites.

In matdoering/openPrimeR: Multiplex PCR Primer Design and Analysis

Identification of Sequence Restriction Sites.

Description

Checks the input sequences seqs for the presence of restriction sites. By removing the restriction sites from a primer set, it is possible to identify the coverage of the primers (e.g. using check_constraints) discounting for the impact of the mismatching bases caused by the insert.

Usage

check_restriction_sites_single(
  primer.seqs,
  template.seqs,
  adapter.action,
  direction = c("fw", "rev"),
  selected = NULL,
  only.confident.calls = TRUE,
  updateProgress = NULL
)

Arguments

primer.seqs	Nucleotide sequences of primers to be checked for restriction sites in terms of a DNAStringSet object.
template.seqs	A DNAStringSet object with nucleotide sequences containing the templates corresponding to seqs.
adapter.action	The action to be performed when adapter sequences are found. Either "warn" to issue warning about adapter sequences or "rm" to remove identified adapter sequences.
selected	Names of restriction sites that are to be checked. By default selected is NULL in which case all REBASE restriction sites are checked.
only.confident.calls	Only output confident calls of restriction sites.
updateProgress	A Shiny progress callback function.
The	primer direction that is checked.

Value

A data frame with restriction sites, if any could be found.

References

Roberts, R.J., Vincze, T., Posfai, J., Macelis, D. (2010) REBASE–a database for DNA restriction and modification: enzymes, genes and genomes. Nucl. Acids Res. 38: D234-D236. http://rebase.neb.com

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