0.16.6 documentation

Complete canonical API text; task articles explain the workflows. Tutorials

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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

Circular plasmid sequence examples

On this page

• Format
• Source

Thirteen one-row data frames generated from every reference FASTA record under examples/plasmid/. The file stem is used unchanged as both accver and the display label; the DNA sequence is copied without biological modification. Feature and restriction annotations are generated at run time with find_common_features() and find_restriction_sites().

Format

A one-row data frame with accver, display label, length, and the DNA sequence. The historical plasmid_example_pUC19c spelling is a compatibility alias of plasmid_example_pUC19, including its accver. It must not be confused with an independently imported GenBank pUC19c record such as L09137.2.

Source

examples/plasmid/.