0.16.6 documentation

Site guide · find your task

Setup and learning paths

HomeInstall and prepare the environmentChoose your learning module

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

Learning map and reference

Articles and complete workflowsFunction referenceReproducible galleryFrequently asked questionsMigrate to the candidate APITerminology and design sourcesDevelopment status and changes

3.3 Features, primers and restriction

On this page

• Prepare this page
• Search and display are separate
• Restriction interpretation
• General feature recognition
• Follow an annotated reference workflow
• Check your result

Search known DNA for primers, restriction sites and common features, then choose a display. Computational matches and experimental validation are different.

Prepare this page

In a fresh R session, run the code below, then follow this page in order. Colours and layout are optional display choices; inputs select only the fields needed.

Code

library(ggchord)
library(dplyr)

Search and display are separate

Use the bundled pUC19 DNA for exact catalogue-primer and selected restriction searches:

Code

data(plasmid_example_pUC19)
target <- setNames(plasmid_example_pUC19$sequence, plasmid_example_pUC19$accver)
primers <- find_primer_bindings(target, set = "universal")
sites <- find_restriction_sites(target, enzymes = c("EcoRI", "BamHI", "HindIII"), methylation = "none")
recognition_seq <- plasmid_example_pUC19 |>
  select(accver, length)
p_sites <- ggchord(seq_data = recognition_seq) +
  geom_seq() +
  geom_primer(data = primers, colour = "#A020F0") +
  geom_restriction_site(data = sites, colour = "#29364B") +
  coord_circular()
p_sites

Search supports circular-origin binding; set circular = FALSE for a linear sequence. The actual pUC19 hits shown here should be inspected in the returned table. Search hits are computational matches, not experimental validation. Primer "three_prime" mode finds an exact suffix, with no mismatch model; its Wallace melting-temperature estimate is a composition heuristic.

Restriction interpretation

find_restriction_sites() returns unfiltered matches and cleavage coordinates; filter_restriction_sites() selects a display set. Enzyme site counts refer to the full supplied sequence and remain stable after filtering. methylation = "auto" uses audited context only for exactly recognized bundled references; it does not claim unknown samples are unblocked. This example explicitly uses "none"; this is a search assumption, not a measurement of methylation in a physical sample. geom_restriction_site(leader = "radial") is the default route.

General feature recognition

find_common_features() supports curated exact-reference annotations, DNA and record-specific matching modes. Protein searches use standard-code six-frame translation; they do not implement splicing, alternative initiation or origin-crossing protein matches. Source genetic-code metadata does not select another translation table. For nonstandard codes use DNA matching or external code-aware analysis. Confidence is a heuristic label, not a probability. Use explicit CDS projection for known protein/genome maps.

Follow an annotated reference workflow

This short workflow uses the same source-backed plasmid as the complete map. The complete pUC19 workflow demonstrates catalogue annotations, exact reference matching, site display filtering, primer labels and feature stacking together. Changing only a sequence name does not make it a recognized reference; sequence content determines source-backed recognition. Read the result methods and methylation provenance instead of assigning reference claims to an unknown sample.

Check your result

Inspect match positions, methods and provenance. Restriction filtering is a display choice; methylation search conditions are not a measurement of an unknown sample.

Continue: A complete circular annotation workflow →