Plasmid Maps and the Sequence Viewer
Open a sequence and you get its map: the bases in rows, the features drawn over them, and the cut sites marked where the enzymes land. This page covers reading that map, the layers you put on it, the tools that run on a stretch of bases you pick out, and getting the picture into a paper.
The Three Views
Views in the sidebar switches between three ways of drawing the same sequence. The buttons read Sequence, Linear, and Plasmid.
- Sequence shows the bases themselves in rows with a ruler and annotation tracks, and it is where a linear sequence opens
- Linear draws the whole sequence as a feature map
- Plasmid is the circular view, and it appears for circular sequences that are not protein
A circular sequence opens on the plasmid map, with its features drawn as arcs around the ring and its cut sites marked outside it.
Layers
Layers overlays computed information on top of whichever view you are in:
| Layer | Default | What it draws |
|---|---|---|
| ORFs | On | Open reading frames on both strands, 100 amino acids and longer, each starting at a start codon and labeled with its frame and length, such as ORF +1 (243aa) |
| Restriction sites | On | The common enzymes, both strands, aware of circularity. The label reads (Scanning...) while it works |
| Translation | Off | Amino acids under CDS and gene features, including the ones the ORF layer found |
| Complement | Off | The reverse strand, under the bases |
Which layers you get follows the sequence type. ORFs and Translation apply to DNA and RNA, Restriction sites and Complement to DNA. A protein sequence has no Layers section at all, because every one of them reads nucleotides.
Translation and Complement grey out on the plasmid map, where there are no base rows to draw them under. Switch to Sequence and they come back.
The two scans start once the page has drawn. Sequence and Linear put the bases up first and land the layers a moment later, and the plasmid map waits for both scans and then draws once, so a large plasmid takes a beat to appear.
Moving Around
Cmd/Ctrl + F searches within the sequence, as text or as a regular expression, and steps through the matches with Prev and Next. Cmd/Ctrl + G jumps to a position on the sequence and plasmid views. Cmd/Ctrl + Z undoes and Cmd/Ctrl + Shift + Z redoes. Escape backs out of whatever is open, one layer at a time, and ends by clearing your selection.
Drag across the bases on Sequence or Linear to select a region, and the status bar tells you its coordinates, length, GC content, reading frame, and, when the selection divides by three, how many amino acids it encodes. The plasmid map reads out the position under your cursor instead.
Working in a Selection
Dragging out a region opens a menu, and this is the most important thing to know about the workspace: several tools live here and nowhere else.
Picking an action closes the menu and keeps the region selected, so Selection tools in the status bar opens the same menu again for the next thing you want to run on those bases. Clear releases the selection.
The menu opens with Comment on selection, which anchors a discussion to those exact bases, and Copy Sequence. Below them the tools sit in three groups:
| Group | On DNA | On RNA | On protein |
|---|---|---|---|
| Create | Add Annotation, Save as New Sequence, Design Primers | Add Annotation, Save as New Sequence | Add Annotation, Save as New Sequence |
| Transform | Reverse Complement, Complement, Translate, Transcribe | Reverse Complement, Complement, Translate, Reverse Transcribe | |
| Analyze | BLAST, Codon Optimize, CRISPR Design, Find ORFs | BLAST, Find ORFs | BLAST |
Save as New Sequence asks you to name the region before it writes anything, then tells you it saved. From there you can Open sequence, or Keep working here to stay on the one you were reading.
The Transform tools and Find ORFs are covered in Sequence Analysis and BLAST, which also has BLAST. Design Primers, CRISPR Design, and Codon Optimize are in Primer and CRISPR Design. All of them open on the bases you selected.
Annotations
+ Add beside Annotations in the sidebar, or Add Annotation in the selection menu, opens the annotation editor. It takes a Label, a Start and End, a Direction of Forward, Reverse, or None, and an optional note. Type is one of nine: Gene, CDS, Promoter, Terminator, Origin, Primer Binding Site, Restriction Site, Feature, and Custom. Each carries its own color onto the map, and Custom is the ninth preset rather than a name you type.
Auto-Detect, in the header of that dialog box when you are creating an annotation on a DNA sequence, opens Auto-Annotate Features. It scans against a library of common parts, T7 and lac promoters, rrnB and T7 terminators, resistance markers, reporters, origins, epitope tags, and ribosome binding sites, then lists every hit for you to tick. Select all takes the lot. Nothing lands on the map until you press Add, so a scan that finds a promoter you know is wrong costs you a glance.
The sidebar lists every annotation with its type and coordinates, and carries a search box and a type filter once there is more than one kind. Each row's menu holds Edit, Hide or Show, and Delete, and a hidden feature stays in the list, dimmed. Hovering a row lights the matching feature on the plasmid map.
Tip: Select an annotation and press Delete to
remove it, then Cmd/Ctrl + Z if that was the wrong one. Adding,
editing, and deleting annotations all undo.
Exporting a Figure
Export Figure in the sidebar's Analysis section writes the map currently on screen, circular, linear, or the sequence rows.
Format is SVG or PNG. Width is the printed width, offered as Single column (89 mm), Double column (183 mm), Slide (254 mm), or Custom anywhere from 10 to 1000 mm, and it starts on double column. Resolution offers 150, 300, and 600 DPI, and starts at 300.
Choose SVG and the map is drawn rather than photographed: feature arrows, the backbone, tick marks and every label arrive as separate objects, and the feature names stay text you can retype. Open it in Illustrator or Inkscape and recolour one feature without touching the rest. It prints at the width you picked whatever the resolution says, since DPI only sharpens a photograph embedded inside it.
Choose PNG and the map is captured at the resolution you picked, then handed to the markup workspace, where you can draw arrows and labels on it before downloading.
The figure carries whatever the map is showing, so the layers you switched on come with it: ORFs, restriction cut sites with their enzyme names, the amino acids of a translated feature, and the complement strand.