ggchord: chord, collinear and plasmid tutorial9 hours ago
Install and prepare the environment | Install and inspect the environment | Which version are you using? | Support evidence | Choose a learning path | Which columns come first? | Optional: check one complete plot | Read the quick result | Optional: save the quick result | Common execution problems | Choose your learning module | Which view should you choose? | Prepare this page | Chord: compare multiple sequences | Collinear: align local comparisons | Circular: annotate one sequence | Check your result | 1.1 Tables and field meanings | Minimal shapes of three tables | Names and optional columns | Inspect real tables | Coordinates and directions | 1.2 Produce and import comparisons | Start with FASTA and GFF3 | Produce your own BLAST results | When another format already exists | 1.3 Build the layers step by step | Prepare this page | Step 1: sequence backbones | Step 2: observed comparisons | Step 3: selected genes | Step 4: label every displayed feature | 1.4 Direction, curvature and clearance | Inspect directional evidence first | Inspect directional evidence | Combine capabilities into a readable view | Why clearance modes look different | Guides and export | 1.5 Filter and summarize links | Prepare this page | Begin with the original link table | Understand each transformation | Density is an explicit statistic | Choose interval ribbons or point links | Check your result | 1.6 Full source-file workflow | Prepare this page | 1. Read and inspect original records | 2. Make the display selection explicit | 3. Build a chord comparison | 4. Inspect all annotations in a linear view | 5. Keep the evidence with the figure | Select fields before passing data | Check your result | Save this result | 1.7 Complete chord showcase | What this view shows | Prepare original records | Compose the layers | Read and adapt the result | Save at its intended size | 2.1 Reuse chord input tables | The same three tables | Obtain the inputs | Current conversion boundaries | 2.2 Switch coordinates and add layers | Prepare this page | Replace coord | Read backbone lengths | Add comparisons | Add strand-separated genes and labels | 2.3 Routes, clearance and the ruler | Prepare this page | Specify controls for long links | Local clearance and dashed outlines | Why the ruler was offset | Continue in depth | 2.4 Compare CDS neighbourhoods | Prepare this page | 1. Extract actual CDS and coding DNA | 2. Declare members and sequence pairs | 3. Focus on comparable neighbourhoods | 4. Project supported protein intervals to both CDS | Check your result | Save this result | 2.5 Focus, anchors and segments | Prepare this page | Focus without losing origins | Independent windows and local reversal | Explicit biological relationships | Map an annotation back to source coordinates | Check your result | 2.6 Complete collinear showcase | Complete result | Prepare original records | Reserve space for connections and labels | Compose the layers | Adjustment and limits | Save at the intended size | 3.1 DNA, annotations and 13 references | Tables and optional information | Inspect bundled real records | Import your own plasmid | A progressive case sequence | 3.2 From a circle to annotation layers | Prepare this page | Step 1: double backbone and centre name | Step 2: feature shapes | Step 3: fitted feature labels | Step 4: primers and selected restriction sites | 3.3 Features, primers and restriction | Prepare this page | Search and display are separate | Restriction interpretation | General feature recognition | Follow an annotated reference workflow | Check your result | 3.4 Thirteen plasmid references | Prepare all cases once | Inputs and recognition results | pSB1C3: Small vector and basic structure | pUC19: Common features and replication origin | pBR322: Multiple resistance regions and direction | pBluescript II SK(+): Local regulation and short features | pET-28a(+): Expression regions and tags | pETDuet-1: Dual expression units; transition to the dense case | pDONR221: Recombination-related architecture | pcDNA3.1(+): Annotation hierarchy in an expression vector | pTRE-Tight-BI: Bidirectional regulatory structure | pTRIPZ: Display density on a longer sequence | pCAMBIA1300: Architecture of a larger plant vector | pEarleyGate 201: Category comparison with another plant vector | pSpCas9(BB)-2A-GFP (PX458): Large expression vector and label fitting | Next | 3.5 Complete plasmid cases | Prepare this page | Use a source-backed sequence | Compose independent layers | Read the annotation layers | Choose the displayed sites deliberately | Understand catalogue and label limits | Adapt the workflow | Check your result | Save this result | Complete example: a dense pETDuet-1 map | Prepare tables and coordinates | Prepare this page | Tables | Coordinate contract | Import original records | Validate, clean, prepare | Inspect a problematic input and its repair report | Declare genome and contig keys | Minimal input and protein alignments | Check your result | Import and convert data | Prepare this page | Adapt an existing table | BED and PAF: convert coordinates once | GenBank: retain record identity | Optional interval objects | Check your result | Import nucleotide and protein alignments | Prepare this page | Use the default tabular columns | File layout and minimal plotting fields differ | Read BLASTp with explicit coordinate units | Sources and limits | Check your result | Project protein intervals to genomic coordinates | Prepare this page | Start with source-backed CDS | Segments, phase and partial regions | BLASTp query spans and two-ended links | Check your result | Features, stacking and genomic decoration | Prepare this page | Preserve feature semantics | Choose shapes by meaning | Highlight an interval without rewriting observations | Check your result | Labels and local placement | Prepare this page | Select a layout | Fixed and automatic placement | Match anchors across layers | Compare the three gene layouts | Check your result | Quantitative tracks | Prepare this page | Compute a track from actual DNA | Draw GC fractions | Share an ID deliberately | Inspect retention and limits | Combine bars, a moving mean and annotation bands | Check your result | Save this result | Mappings, scales, guides and themes | Prepare this page | Build styles from data roles | Fixed styles and user scale priority | Make legends readable | Select a theme for the scene | Check your result | Set values by sequence and strand | Prepare this page | The capability remains supported | Supported parameters | Compatibility and design tradeoffs | Check your result | Common adjustments and grammar | Prepare this page | Assign each responsibility | Map link identity | Place features | Check your result | Export, preview and diagnostics | Prepare this page | Save the intended size | Consume geometry by name | Interpret evidence | Complete layout, tables and opt-in ordering | Check your result | Articles and complete workflows | Three learning paths | Read in order or consult as needed | Setup and learning paths | Module I · Chord | Module II · Collinear | Module III · Plasmid | Consult as needed · Data and layers | Learning map and reference | Capabilities and runnable evidence | Reproducible gallery | Find a figure by task | Figures and dimensions | One source for both languages | Reproduce | Asset sources | Frequently asked questions | Why are labels different after resizing? | Why did an old parameter stop working? | Why is a feature rejected as a gene? | Why is a ribbon missing in linear mode? | Can the package compute alignments or validate primer experiments? | Is a measured diagnostic a release certification? | Where should I report a problem? | Migrate to the candidate API | Scope and timing | Replacement table | Run the replacement | What remains supported | Terminology and design sources | Shared terminology | Design and asset provenance