Viewing and selecting

The toolbar's view switcher shows the Sequence view, the Map, or Both side by side. The two views share one selection: whatever you select in one is highlighted in the other and reported in the status bar as N bp selected, from to to, GC p % (1-based, inclusive). A selection through the origin of a circle ends at a small number (591 to 20 on a 600 bp plasmid), and every panel that names a range writes it the same way.

The switcher, the Complement (Alt+C), Translations (Alt+T) and Cut sites (Alt+R) toggles next to it, the Format menu's choices (the GC track and its window among them), the Edits baseline and the sizes of the panes are remembered in the browser, so the views come back the way you left them the next time you open PlasmidPop. They are settings of the app, not of a document: they do not change with the file you open and are not written into a saved file.

Sizing the panes

In the Both view the boundary between the map and the sequence can be dragged: take hold of the line between them and move it. The same handle sits on the sidebar's inner edge. Each pane has a floor it will not be dragged below, so it is never squeezed to a sliver.

Drag the line to move it. Double-click it to put that one boundary back where it started.
Drag on past the floor to put the pane away: more than half of it gone, and the map or the sequence leaves the other one showing alone (the view switcher's Sequence or Map), and the sidebar folds to its tab rail. The view switcher and the rail bring them back.
With the handle focused, the arrow keys move it in small steps, Page Up and Page Down in larger ones, and Home and End take it to either floor; one more arrow toward a pane at its floor puts it away. Alt+B takes the keyboard to the next handle from wherever it is, and Escape gives it back — no need to Tab through the toolbar to get there.
On a narrow window the map sits above the sequence instead of beside it. That layout keeps its own boundary: a division chosen for a wide window is not imposed on the other one. On a window narrower still the sidebar moves under the editor, and its top edge is a handle too; its height is kept apart from its width beside the editor.
Format ▸ Reset the layout puts the map, the sequence and the sidebar back to the sizes they started at, and opens the sidebar if it is closed.

Clicking the sidebar tab that is already open closes the panel and leaves the tab strip on the window's edge, giving the views the whole width. Clicking any label opens it again on that tab, and Alt+S does both. The panel keeps whatever you had typed into it while it is closed.

Which panel is open belongs to the document tab, not to the window: switching files brings back the panel that file was left on, and a file opened while you are working in one panel opens on the same one. So setting up a digest in Cloning and opening the insert alongside it keeps you in Cloning, and looking at the insert's features does not move the first file.

On a phone

On a screen narrower than about 600 px PlasmidPop is a reader rather than an editor: it shows one pane at a time, chosen from a bar at the foot of the screen. It is meant for the plasmid someone sent you as a link, read where the message arrived.

Map, Sequence and Details are the three panes. Details holds the Features and Enzymes lists; the other sidebar tabs (primers, alignment, cloning, ORFs, translation, history) are for making things and are not offered on a phone.
The toolbar keeps the name, the size and shape of the molecule and the File menu, so a document can still be downloaded or sent on as a link. The view switcher, the toggles, Format, Edits and History are not there.
Tap a feature on the map to select it. Its name comes back if the ring had no room for it and stays until you tap somewhere else, which is what hovering does with a mouse. Tapping a feature's name does the same, with the name and its leader drawn out. Pinch to zoom and drag to pan.
In the sequence a finger scrolls. A tap on a feature bar selects the feature, a tap on the bases puts the caret there. The bases are shown alone: the Complement and Translations toggles are not applied, since each one adds a line to every row.
To copy a stretch of sequence, press and hold on its first base for half a second, until that base is selected, then drag to its last one without lifting; holding near the top or bottom edge scrolls on. When you lift, a Copy button over the selection copies its bases, ready to paste into a message or another app. A quick drag is still a scroll and a quick tap still a tap. A tablet does the same.
Cut sites are hidden on a phone to begin with, so the map and the bases show the features and a tap lands on what you meant. To see them, open Details ▸ Enzymes and tap Show cut sites; the phone remembers that. The choice is the phone's own: the Cut sites toggle on a wider window keeps whatever it was set to there.
Each tab remembers its pane: switch to another document and back, or reload the page, and it is on the pane you left it on. A document you open — a file, or a link someone sent — starts on the Map.
Tapping a row in a list takes you back to the view you were last in, with that feature selected. The Features list has no Rename, Edit or Remove on a phone, so a stray tap cannot turn a plasmid someone sent you into a working copy.

To open a GenBank file that arrived as a mail attachment, share it to PlasmidPop from the mail app, on Android with PlasmidPop installed: see Opening an attachment from another app.

Nothing about a document is different on a phone: it is the same file, stored in the same browser, and everything comes back on a wider window. A notice says so the first time; Got it puts it away for good. A tablet is wide enough for the normal layout, with the map above the sequence in portrait, and the same touch gestures work there.

Sequence view

Bases are laid out in rows that fill the available width — or a width you fix in the Format menu, below — with a ruler above each row giving the position of its first base. Below each row:

the complement strand, when Complement is on in the toolbar;
for a document whose molecule type is RNA (a .rna file, or a GenBank record with RNA on its LOCUS line), both strands are drawn with U where the stored sequence has T, and the complement of A is U. This is only how the letters are drawn, in the view and in its SVG and PNG exports: the sequence itself, copying, downloads, enzymes, primers, translation and search all keep working on T, and a DNA/RNA hybrid is drawn as DNA;
one line of amino acids per CDS feature, when Translations is on (see Translation);
features as coloured bars with their names, stacked into lanes when they overlap;
cut sites of the enzymes ticked in the Enzymes tab, as marks with the enzyme name, unless Cut sites is off in the toolbar (see Restriction enzymes);
the GC content track, when Format ▸ GC content track (Alt+G) is on: a line of the GC fraction under the strands, one point per base, with a hairline at 50 %; see GC content;
edit marks over the bases you have changed, when Edits is on in the toolbar (see Editing the sequence);
a preview, outside everything else: dashed spans in a colour of their own, drawn while a panel is pointing at something that is not in the document — a primer pair you are weighing up, every match of a find. See Previews.

The first and last rows also show the sticky ends of a molecule that has been cut: single-stranded bases are washed over with a gap opposite them, and an overhang on the other strand is drawn just outside the first or last column (see Simulated cloning).

Clicking a feature bar selects that feature; clicking an amino acid on a translation line selects that residue's three bases. The pointer turns into a hand over those tracks and stays a text cursor over the bases, where it places the caret. Lowercase bases stay lowercase, as many people use case to mark regions.

File ▸ Export figure…, with Sequence view chosen, writes what you see as an SVG vector file, a PNG picture or a PDF for figures — the whole sequence, the selection or a range, at a chosen number of bases per row, on A4 or US Letter pages if you like; see Exporting.

GC content

Format ▸ GC content track (Alt+G) adds a track of GC content. In the sequence view it is a band under the strands of each row, with a line for the fraction of G and C in a window centred on each base and a hairline at 50 %. On the map it is a ring just inside the feature lanes, with hairlines at 0 and 50 %; the name in the centre makes room for it. Hover the track for the exact value, the window and the base. It is for DNA and RNA; a protein has none, and the phone's reader leaves it out.

The window is Automatic until you choose one under the toggle (10 to 1,000 bases): 50 bases in the sequence view, and about 1 % of the sequence (at least 10 bases) on the map, where a window as short as the sequence's resolution would be noise. On a circular sequence the window wraps the origin, so the line is continuous across it; at the ends of a linear sequence it is the half window that exists. Ambiguity codes count for what they could be: S is GC, W is not, R, Y, K and M are half, and N says nothing and is left out. Both the track and the window are remembered in this browser. A long sequence (over 200 kb) is worked out in the background, and the track appears when it is ready.

The status bar also gives the GC of whatever is selected, whether or not the track is on: 1,200 bp selected, 101 to 1,300, GC 52.3 %. On a circular sequence a selection across the origin is counted across it.

Previews

Some things are worth seeing on the sequence and the map before they are anything in the document. A previewed span is drawn dashed, in a colour used for nothing else: in the sequence view in a band outside the feature lanes, on the map in a ring just inside the backbone, where a span too short to see is widened as a short selection is.

Nothing previewed is part of the document. It is not saved, it is not in the SVG exports, it costs no undo step, and it goes away when you edit the sequence or close the panel that asked for it. Switching to another sidebar tab takes it off the views too, and coming back brings it back: what the panel was showing is kept for each document while the page is open. Two panels can preview at once — the find bar and a sidebar tab, say — and their spans are drawn together.

A primer's arrow is marked in the colour of a changed base wherever the primer does not pair with the sequence under it, so a mismatch is seen where it is rather than counted in a list.

Today these use it:

the Primers tab, for a designed pair and the product it would give, and for the binding sites of a primer you paste in;
Find, which draws every match at once while the bar is open;
the ORFs tab, which draws every open reading frame it lists; click one on the map or in the sequence view to select it;
the Cloning tab, which draws the pieces a digest would give, each with a tick where its cuts fall, and draws the one under the pointer as a solid arrow. These can be clicked, which puts that fragment on the shelf, for the Bench; and its PCR, which draws the products and primer sites.

Format

The toolbar's Format menu (Alt+O) sets how the sequence view draws. It is laid out as a list of settings: each setting is one row, with its choices side by side on the right, so every choice is in view and one click away. Choices take effect at once and the menu stays open, so you can try one and look. Tab walks the rows and the arrow keys move along a row's choices; Escape closes.

Sequence view — the strands themselves:

Text size — Small, Medium (the default) or Large. The rows, lanes and labels scale with the text, so a larger size gives a roomier view with fewer bases in a row.
Bases per row — Fit (the default) puts as many bases in a row as the width holds, in tens, and re-flows when the window changes. Pick 30, 60, 90 or 120 instead to keep the same rows whatever the window size — useful for comparing two windows side by side, or for an export that matches what you see — or type any count from 10 to 1,000 in the Other box under it and press Enter. If the fixed width does not fit, the view scrolls sideways.
Number the complement repeats each row's position number beside the complement strand, so a wide row can be read from either line.
Colour the bases gives A, C, G and T each their own colour on both strands; anything else (an N or another IUPAC code) is grey. While it is on, the four swatches under it choose the colours, for the sequence view, a read's trace and the SVG export alike; Reset goes back to the theme's, which differ between light and dark.

Tracks — what is drawn around the strands:

GC content track (Alt+G) draws the GC content under the strands in the sequence view and as a ring inside the map; Window under it sets how many bases it is averaged over. See GC content. Greyed out for a protein.
Residue numbers — Every 10th (the default) numbers the first residue and every tenth one above the amino acids under each CDS; All numbers every residue; Off leaves the numbers out and gives the rows back the room they took. See Numbered residues. Greyed out for a protein, whose ruler already counts its residues.
Trace — Hidden, Short or Tall, for the chromatogram of a sequencing read; see Reads. Greyed out unless a read with a trace is in front.

Under a separator, two items that are not about the sequence view:

Reset the layout puts the panes back to the sizes they started at, see Sizing the panes.
Keyboard shortcuts… opens the table of every key, where a binding can be changed; see Keyboard shortcuts.

The SVG exports follow the bases-per-row, numbering (residue numbers included) and colour choices, chosen colours included. They keep their own text size and font so the file looks the same whatever the screen is set to. All of these are remembered in this browser.

Circular map

The map draws the backbone as a ring with tick marks, features as arcs in lanes around it, and labels with leader lines. Features that share a name (a gene and its CDS, for example) get one label, and a gene and CDS of the same name on exactly the same bases are drawn as one bar, the CDS's, in both views; the feature list still lists both. Cut sites of the ticked enzymes are labelled on the same ring, unless Cut sites is off in the toolbar. The centre shows the name and length when they fit whole; on a narrow map the name is set smaller, and past that it is left out rather than squeezed or cut short, since the toolbar has it. Under the name the length reads "5,432 bp circular" or "5,432 bp linear", dropping the topology on a map too narrow for it.

A linear sequence is drawn as an open ring with a wide gap (24 degrees, at any map size) at the top. The sequence is laid out over the rest of the ring, so the features, ruler, selection and clicks all stop at its two ends and nothing is drawn or can be clicked in the gap. Each end has a cap across the backbone and a number: 1 at the left end and the length at the right.

Nothing is too small to see. A feature of a few bases, less than a pixel of ring on a large plasmid, is drawn as a narrow mark at least three pixels wide, and it can be hovered and clicked at that width. A selection that short, and the cursor itself, are drawn as a needle from outside the backbone in through the lanes, so they are not lost under a feature.

Click the backbone to place the cursor, drag along it to select. On a circular sequence the selection runs clockwise from where you started and may cross the origin.
Click a feature arc to select the feature; if the Features tab is open, its row is highlighted on its own and scrolls into view — even where another feature covers exactly the same bases, as a gene and its CDS often do. Double-click the arc to zoom in on it.
A label is a target too: clicking a feature's name selects the feature, double-clicking it zooms in on it, and clicking a cut site's name, or its tick mark on the backbone, puts the cursor at the cut. Hovering one highlights it and its leader.
Click empty space — inside the circle, or outside it — to clear the selection.
Wheel or pinch to zoom about the pointer; double-click empty space to zoom in one step. When zoomed in, drag empty space (or drag with the middle button) to pan.
The buttons in the corner zoom + and −, zoom to the Selection and Fit the whole map.
A selection too short to see as an arc — a few bases of a plasmid, say — is drawn a little wider than it is and marked with a line running from the backbone in towards the centre, so it can still be found. Zoom in to see its true extent.
When Edits is on, your changes are marked on the ring: bands over the backbone where bases are new (green) or replaced (amber), a red wedge where bases were removed, and an outline on any feature you added or edited. See Seeing what you changed.

Lane widths and fonts do not change with zoom; the tick marks get denser as you zoom in.

When there are more labels than room

Every label — a feature's name, a cut site, one of the ruler's position numbers — is kept clear of every other one. A label that cannot sit beside the thing it names slides along the ring until it finds room, so it stays on the same side of the map and never crosses the circle. It slides a short way only: a name a long leader line away from its own tick is harder to read than no name at all, so past about eight lines' worth the map leaves it out instead of towing it to the end of a crowded arc. A bunch of labels shares out the room around it: the bunch spreads about its middle, so the labels at its edges are not squeezed out by the ones in the middle, and one crowded against the top or bottom of the circle moves away from it together. The labels stay in the order their ticks are, and their leader lines do not cross; where two features sit at nearly the same place one of them has to give way, and it is either drawn with a leader that crosses its neighbour's or left out. A label with no room beside the ring can go a little further out, on a second row or column outside the first, where its leader can reach it without running through another label. The same document is laid out the same way every time it is opened.

Past a certain number of labels the ring is full, and the map leaves some out rather than writing them over each other. It says how many in the bottom-left corner: +7 labels not shown. What is left out is decided by the document, not by where the crowding happens to be: features keep their labels before cut sites do, longer features before shorter ones, and a rare cutter before an enzyme that cuts all over the plasmid.

Nothing is lost by it. Hover a feature arc or a cut site's tick mark and its name appears even if the ring had no room for it, drawn in a rounded outline so that it reads as lying on top of the map rather than as a hole in it. The feature list and the Enzymes tab list everything either way. Zooming in also frees up room, since a label whose feature has gone off screen no longer takes a slot.

The SVG map export does not leave labels out — a figure has nothing to hover. It grows its canvas around the same circle until they all fit instead, so an exported map may be a little wider than it is tall, and it lets a label sit further from its feature than the map on screen would, for the same reason: on paper a name that did not fit is gone for good. A map with hundreds of feature lanes gets a canvas big enough for the whole circle, so it is never exported blank.

Selecting

In the sequence view:

Click between two bases to place the cursor there. The status bar says Cursor after base N.
Drag to select a range; Shift+click extends the selection to the clicked position.
On a translation line, click an amino acid to select its codon and drag along the line to extend the selection codon by codon, so the selection always starts and ends on a codon boundary. On a reverse-strand CDS the codons are read right to left, and the selection follows. Dragging off the coding bases — into an intron or past either end — leaves the selection as it was.
Shift+Arrow keys extend the selection one base (left/right) or one row (up/down) at a time. Home and End go to the ends of the row, Ctrl+Home and Ctrl+End to the ends of the sequence; add Shift to select on the way.
Ctrl+A selects everything. Escape clears the selection.

Elsewhere:

Clicking an entry in the Features, Enzymes, ORFs, Primers or Cloning tabs selects the corresponding range and scrolls both views to it.
Find selects each match in turn.

Many actions work on the selection: Add feature, Delete selection, Copy and Cut, Export selection, Translate, Design primers, Align against selection.

When you let go of a selection in the sequence view, a small bar appears beside it with the commonest of these: Style ▾ (see Colouring and enlarging bases), Case ▾ (see Typing, deleting, replacing), Add feature and Copy, and how many bases are selected. It sits above the selection, or under its last row, below that row's translations and feature lanes, where there is no room above for the Style menu, so the selected bases stay in view while you work on them. A selection whose first and last rows are both out of view (Ctrl+A on a long sequence, say) keeps the bar at the top of the view as you scroll. While the mouse is elsewhere (a selection made on the map or from a panel) the bar is faded; it comes back in full as soon as the mouse is over the sequence. Clicking a single position, or selecting nothing, puts it away. The phone reader has its own Copy after a long press instead.

The checksum

The right of the status bar shows a short checksum of the open molecule, like cdseguid=dUxN7Y…. Click it to copy the whole thing.

It is a SEGUID v2 name, and it has one property that makes it worth having: it does not change when the molecule is written differently. A plasmid has no first base, and DNA has no top strand, so rotating a circle to another origin or reverse-complementing it gives a file that shares no text with the one you started with — and the same checksum. Two molecules with the same checksum are the same molecule; two with different checksums are not.

The prefix says what kind of molecule it is: cdseguid= for a circular one and ldseguid= for a linear one. It is part of the checksum, not a label on it — the same bases as a plasmid and as a fragment are two different things.
Sticky ends count. A fragment left by a digest is not the blunt fragment of the same bases, so its checksum is different. Case does not count: atgc and ATGC are the same molecule.
Names, features and everything else are not in it. It is a name for the sequence, not for the annotation, so renaming a feature does not change it and neither does adding one.

Paste it into a lab notebook, an email or a methods section and anyone with the same construct can check they have the same construct — without either of you sending the other the sequence. Compare with… shows both checksums, and uses them to line a rotated plasmid up with this one before showing the differences.