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Editing the sequence

The sequence view is a text editor for DNA. Click to place the cursor, then type. Features keep their places: a feature after an insertion moves along, a feature around it grows, a feature whose bases are deleted shrinks or disappears. A CDS that loses bases from the start of its reading (its left end, or its right end on the reverse strand) has its /codon_start moved on to the first whole codon left, so the translation keeps its frame, and is marked 5′-partial, since what is left has no start codon of its own: the next codon is read as itself, not as M. (Losing only the bases a /codon_start of 2 or 3 skips leaves the start codon whole, so the CDS stays unmarked.) A CDS that loses bases from the end of its reading is marked 3′-partial in the same way, since what is left has no stop codon of its own.

Typing, deleting, replacing

Copy, cut and paste

Ctrl+C copies the selected bases and Ctrl+X cuts them. The features that fall inside the selection travel with the bases, trimmed to it (the source feature is left behind). Ctrl+V pastes at the cursor or over the selection, and the features arrive shifted to the new position. A paste is a single undo step.

Colouring and enlarging bases

To make a stretch of bases stand out, select it and open Style ▾, on the bar that appears beside the selection or in the edit bar (Alt+Y):

The menu ticks what the whole selection has in common, and stays open so you can try one choice after another. Each choice is one undo step.

A style belongs to its bases, not to a position. It moves when you type before it, grows when you type inside it, goes when its bases are deleted, comes along when you copy and paste them, and turns over with Reverse complement. A style is not a feature: it takes no lane, is not in the feature list and is not drawn on the map. It is kept with the document, in its GenBank file (as a comment other programs ignore) and in a share link. FASTA has nowhere to keep it. It shows in the sequence view and in its SVG export.

Whole-sequence operations

In the edit bar:

On a molecule with sticky ends (a fragment from a digest, see Simulated cloning), an edit that reaches the very first or last bases leaves that end plain and blunt again, since it is no longer the end the enzyme made; an edit in the middle leaves both ends as they were. Making the molecule circular drops the ends, and reverse-complementing swaps them — and moves the sequence with them. The sequence shown is the top strand alone, and the two strands of a sticky-ended molecule do not cover the same bases, so turning it over writes out the other strand, which starts and ends elsewhere: the bases of an overhang the bottom strand carried come into the sequence and the ones only the top strand had leave it. The molecule is the same one; its length changes by an overhang at each end, and a feature annotated on an overhang that has gone goes with it. A blunt molecule is simply reversed.

To rename the document, click its name in the toolbar, type, and press Enter (Escape cancels).

Seeing what you changed

The Edits button in the toolbar marks your changes in both views, like tracked changes in a word processor. Bases that are new are tinted and underlined in green, bases standing where other bases used to be in amber, and a red wedge with a line through the strands marks every place where bases were removed. A feature you added or edited gets an outline in the same colours, and the line says which kind of edit it was: a solid outline means the feature covers different bases than it did, a broken one means the same bases described differently — retyped, renamed, a qualifier edited. The first can break a construct and the second cannot, which is the one distinction a line can carry. A base added to or removed from a run of identical bases (AAAA) beside a feature's edge does not outline the feature, wherever in the run the edit is drawn: it covers the same bases either way. Its ends must still agree on one place for the edit, so a feature whose start or end was then moved by hand is outlined. Nor does replacing a few bases with longer or shorter text (T with CT, GAA with A), across the origin of a circle too, outline a feature the editor left where it was, though the bare sequences would also read the first edit as C inserted before the feature and the second as GA deleted. The dot on the button says something is marked; its tooltip, and the foot of its menu, count it up (+12 bp · 4 bp changed · −3 bp).

A new name or a change between linear and circular touches no base, so there is nothing in the views to mark; the toolbar marks it instead, where the name and the shape are written. The name or the word _circular_ gets a broken amber underline, the line of a feature relabelled over the same bases, and its tooltip says what it was (Renamed from “pBR322”, Was linear); the Edits tally adds renamed or made circular. It follows the menu like the other marks: nothing while they are off, and against the file you compared with it says what that one is called or is (Named “pBR322” in theirs.gb). The name a working copy takes by itself (pBR322 copy) is not counted as a rename — the banner above the views already says it is a copy.

The circular map marks the same changes on the ring, in the same colours: a green or amber band drawn over the backbone where the bases are new or replaced, and a red wedge pointing at every place where bases closed up. A stretch too short to see as a band — a single base of a plasmid — is drawn a little wider than it is, the way a short selection is. Features keep their outlines there too, broken or solid as in the sequence view. This is the view that answers _where_ a change landed: in the marker, in the origin, in nothing that matters.

A feature you removed is drawn as a ghost: a broken red outline in the feature lanes where it was, with no fill and no arrow. A ghost never takes a live feature's place — it goes in a lane with room there, or in a lane of its own further in — and it has no name in the label ring, so turning the marks on never moves the other labels; point at it and its name comes up (tet removed). Features that went because their bases were deleted get no ghost: the red wedge stands for them, and pointing at the wedge says how many it took (300 bp deleted, with 2 features).

The marks on the map are clickable. Click a green or amber band and its stretch is selected, a wedge puts the cursor where the bases closed up, and a ghost selects the bases the removed feature covered — the same selection Next change would make, so a change across the origin is selected whole. The pointer turns into a hand over a mark, and the mark says what it is (40 bp inserted). A feature, a label or a cut site under the pointer still comes first — clicking a cut site's tick over a mark puts the cursor at the cut, as hovering it shows its name — and pressing on a band and dragging still selects a range as it does anywhere on the backbone. The sequence view's marks are not click targets: a changed base there is a base you may want to put the cursor in.

The menu chooses what the marks are measured from:

The choice is remembered between sessions (except Mark from here and Compared with, which belong to one session's work and come back as Since opened). The marks also appear in File ▸ Export figure…, on the map and in the sequence view alike, and in the review before a download and in Compare with….

Next change (Alt+N) and Previous change (Alt+Shift+N) in the same menu go from the cursor to the next or previous marked change, whatever the marks are measured from: a stretch of new or replaced bases is selected, a place where bases were removed gets the cursor, and both views scroll to it. At the last change Next goes round to the first. On a plasmid, a change that runs across the origin is one stop, selected across it. With nothing marked both are greyed out and the keys do nothing.

The marks describe the difference between two versions, not the steps that got you there: if you type a base and delete it again, nothing is marked. Set origin here renumbers the whole sequence, which makes every base differ from the old version, so the whole sequence is marked and the tally says _too different to follow in detail_. Undo it, or use Mark from here, to get back to useful marks.

Reverse complement is recognised instead: the marks are worked out against the old version turned over too, so a turn on its own marks no bases, the tally says _turned over_, and edits made before or after it are marked as usual. That holds for a sticky-ended molecule as well, whose length changes but whose molecule does not.

Undo, redo and the history list

Undo works on the document in this browser. It does not reach back into a file you have already downloaded, and the browser's autosave always keeps the current state.

The history is kept too, beside the document in this browser's storage, so reloading the page, a crash, or closing the tab and reopening the document from Recent files brings the undo history back: every step, the ones you had undone as well, which Redo still reaches. A run of typing interrupted by the reload is finished: the next key you press starts a step of its own. Up to 200 steps are kept, and at most about 4 MB per document; past that the oldest steps are left out of the stored copy (a plasmid's history is a few tens of kilobytes, so this only happens to genome-sized documents, and one of more than about four million bases keeps no history at all). The history never leaves the browser: it is not written into the downloaded file or a share link, and Remove on the start screen deletes it with the document. See History.