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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 restriction pattern matches and cleavage coordinates

On this page

• Usage
• Arguments
• Value
• See also

Find restriction pattern matches and cleavage coordinates

Usage

Code

find_restriction_sites(
  sequence,
  enzymes = NULL,
  patterns = NULL,
  circular = TRUE,
  database = NULL,
  methylation = c("auto", "none", "dam_dcm")
)

Arguments

sequence

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

enzymes

Optional enzyme names. A data frame is a compatibility spelling for patterns.

patterns

Optional custom definitions.

circular

Allow recognition and cleavage coordinates to wrap origin.

database

Optional parsed pattern database.

methylation

Methylation context. "auto" uses the audited context for recognized reference plasmids and otherwise makes no blocked-site claim; "none" disables blocking; "dam_dcm" evaluates source-backed Dam/Dcm sensitivities against the supplied sequence.

Value

One row per pattern match without display filtering or deduplication. Methylation-aware columns include methylation_status, blocked_by, display_warning, methylation_motif, and sensitivity_source. enzyme_site_count records the number of distinct cleavage/display positions for that enzyme on the complete supplied sequence, so it remains stable after display filtering. For an exactly recognized bundled reference sequence, the reference_enzyme_profiles attribute records its saved display set for use by filter_restriction_sites().

See also

ggchord_data_contract