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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

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Find common biological features in DNA sequences

On this page

• Usage
• Arguments
• Value
• See also

Searches the built-in common-feature database (or a compatible custom database) using curated exact-sequence annotations, exact DNA, and the detection mode stored for each database record. Restriction sites are intentionally outside this API; use find_restriction_sites() for those. Protein matching uses a standard-code six-frame translation, without alternative initiation, splicing or origin-crossing protein matches. Source geneticCode metadata does not select a translation table. For nonstandard codes use mode = "dna" or external code-aware analysis. confidence is a deterministic heuristic label, not a probability or experimental confirmation. identity and coverage describe the reported match method, not independently validated biological function.

Usage

Code

find_common_features(
  sequence,
  database = NULL,
  types = NULL,
  features = NULL,
  circular = TRUE,
  mode = c("auto", "dna", "protein"),
  min_protein_identity = 0.9,
  min_protein_coverage = 0.8,
  resolve = c("best", "all")
)

Arguments

sequence

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

database

Optional normalized database list or custom data frame.

types, features

Optional feature-type and feature-name/ID filters.

circular

Search across the sequence origin.

mode

Matching mode. "auto" first uses curated annotations for an exactly known sequence, then follows each record's detection mode. Records marked exactProteinMatch use exact protein followed by near-exact DNA; other records use exact DNA. "protein" explicitly enables exact and approximate protein matching.

min_protein_identity, min_protein_coverage

Approximate protein thresholds, each one finite number in [0, 1].

resolve

Return deterministic best annotations or every candidate.

Value

A data frame directly usable by geom_feature() and geom_feature_label_repel(). feature_class and feature_shape provide semantic metadata and a geometry hint; neither affects radial stacking. Explicit user aesthetics and scales still take priority. Its segments list-column preserves the biological feature's segment structure.

See also

ggchord_data_contract