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Module I · Chord

1.1 Tables and field meanings1.2 Produce and import comparisons1.3 Build the layers step by step1.4 Direction, curvature and clearance1.5 Filter and summarize links1.6 Full source-file workflow1.7 Complete chord showcase

Module II · Collinear

2.1 Reuse chord input tables2.2 Switch coordinates and add layers2.3 Routes, clearance and the ruler2.4 Compare CDS neighbourhoods2.5 Focus, anchors and segments2.6 Complete collinear showcase

Module III · Plasmid

3.1 DNA, annotations and 13 references3.2 From a circle to annotation layers3.3 Features, primers and restriction3.4 Thirteen plasmid references3.5 Complete plasmid cases

Consult as needed · Data and layers

Prepare tables and coordinatesImport and convert dataImport nucleotide and protein alignmentsProject protein intervals to genomic coordinatesFeatures, stacking and genomic decorationLabels and local placementQuantitative tracksMappings, scales, guides and themesSet values by sequence and strandCommon adjustments and grammarExport, preview and diagnostics

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Find sequencing-primer binding sites

On this page

• Usage
• Arguments
• Value
• See also
• Examples

Searches each distinct oligonucleotide once on both target strands and then attaches all catalogue aliases. Exact matching is the default. Optional three_prime matching uses the longest exact 3-prime suffix available, with no mismatches, and is intended for inspecting partial annealing rather than silently treating it as a full match. Binding hits are sequence-search results, not experimental validation. melting_temperature uses the Wallace composition estimate unless source annotations supply it; ambiguous bases do not contribute to that estimate.

Usage

Code

find_primer_bindings(
  sequence,
  primers = NULL,
  set = c("universal", "all", "reference"),
  match = c("exact", "three_prime"),
  min_annealed_bases = 15L,
  circular = TRUE,
  unique_only = FALSE
)

Arguments

sequence

DNA text, a named character vector, or a data frame with accver and sequence.

primers

Optional custom primers with sequence and optional name and primer_id (one ID per distinct sequence), or a named character vector.

set

Bundled catalogue subset. reference returns authoritative primer annotations from a recognized bundled reference plasmid.

match

Full exact matching or longest exact 3-prime annealing.

min_annealed_bases

One finite integer of at least 8, the minimum suffix length for three_prime matching. Fractional values are rejected.

circular

Allow matches to cross the sequence origin.

unique_only

Keep only primer sequences with one binding site per target.

Value

One row per binding site. The aliases list-column preserves every catalogue name associated with the matched oligonucleotide.

See also

ggchord_data_contract

Examples

Code

target <- c(circle = "TTGCAAAAACG")
find_primer_bindings(
  target, primers = c(test = "ACGTTGCA"),
  min_annealed_bases = 8
)