Insert sequence

Type bases or residues into the sequence at the caret, or replace what you have selected — with live cleaning of what you type, and no silent loss of it.

What it doesCopy Anchor Link

This is the prompt that appears when you type into a sequence. It has two forms, and it tells you which one you are in before you commit:

• Insert — with a caret between two bases, what you type goes in after that position. The prompt counts what you have typed as you type it: "press ENTER to insert 24 bases after base 1,208".
• Replace — with a region selected, what you type replaces it, and the prompt names the region and its size: "press ENTER to replace 36 bases between 400 and 435".

Editing a sequence directly is a real edit to a real molecule, so the prompt is explicit about the consequence before it happens rather than after.

When you'd use thisCopy Anchor Link

• Fixing a sequencing discrepancy — correcting a base you have confirmed is wrong in the record.
• Adding a short element by hand: a linker, a tag, a restriction site, a start codon, a stop.
• Patching a construct before running a simulation on it, when the change is small enough that building it through a cloning tool would be more work than it is worth.

For anything larger than a patch, the cloning tools are the better path: they record what was joined to what, and this does not.

What this computesCopy Anchor Link

This panel edits rather than measures, so what it derives is what your typing is allowed to be:

• The alphabet of the open record, which decides what the field accepts — bases for a nucleotide sequence, amino acids for a protein record — with the placeholder saying which
• The edit itself, applied through the editor, with the inserted or replaced region left selected so you can see what changed

What it refuses, and how: characters that are not valid for the record's alphabet are cleaned out as you type and the field flashes, so a dropped character is visible rather than leaving you wondering why a paste came out short.

Where it livesCopy Anchor Link

It opens by itself when you type into the sequence view, docked in the right rail — not floating over the sequence you are editing. Enter commits. Escape closes, and if you have typed something it asks first (see below).

Inputs and outputsCopy Anchor Link

In: what you type. For a nucleotide sequence the field takes bases; for a protein record it takes amino acids, and the placeholder says which.

Out: the edit, applied to the sequence in the editor, with the inserted or replaced region left selected so you can see what changed.

What it refuses, and what it says:

• Characters that are not valid for the sequence's alphabet are cleaned out as you type, and the field flashes so you can see that something was dropped rather than wondering why your paste is shorter than the clipboard.
• An insert over the size limit is refused with a message naming the limit, rather than being truncated to fit.
• An empty field cannot be committed — the button is disabled and says why.

Typed-but-not-inserted text is treated as an unsaved edit. Pressing Escape with something in the field offers to insert it, discard it, or go back — it does not quietly throw away what you typed. That is the same rule every other panel in the workbench follows for unsaved work.

ControlsCopy Anchor Link

The scienceCopy Anchor Link

There is no algorithm here — the interesting part is the bookkeeping, and it is what makes an edit safe:

Annotations move with the sequence. Inserting bases inside or before a feature shifts everything downstream of the insertion point, so features, primers, parts and translations keep describing the same biology rather than sliding off it.

Coordinates in the prompt are the ones on screen. The positions named — between 400 and 435, after base 1,208 — are 1-based inclusive, matching the sequence ruler and every other readout in the editor, so you never have to convert between two conventions in your head.

An edit is undoable as one step, not as one step per character, and it lands in the document's history like any other change.

LimitationsCopy Anchor Link

• It is a raw edit. No provenance is recorded beyond the edit itself: nothing says the bases came from a particular oligo or a particular clone. When that matters, build the construct with a cloning tool instead.
• No validation of meaning. Inserting three bases into a coding sequence will not warn you that you have added a residue, and inserting one will not warn you that you have shifted the frame. Translate the region afterwards, or use the tools that check reading frames.
• One position at a time. To make the same change at several places, repeat it — there is no find-and-replace over the sequence here.

RelatedCopy Anchor Link

In this group: Edit annotation · Enzyme · Merge features · Manage enzymes · Dot plot · Dot plot grid · Melt curve · Amplification curves · Population genetics · RNA-seq · Site avoidance heat map · Protein coverage · Reference-gene stability · Digital PCR · Codon usage matrix · Pairwise distance distribution · Nearest-neighbor distances · GC content distribution · Base composition per cycle · Pairwise distance grid · Per-cycle channel occupancy · Grammar assembly plan · Gibson assembly plan · Assembly plan build order · Golden Gate assembly plan · Guide track · Primer binding track · Hydropathy profile · Charge vs pH · Amino-acid composition · Hydrophobic moment · Optimization profiles · Digest gel · Virtual gel · Initiation-window fold · Antibody domain map · Electropherogram · Circuit netlist · Circuit transfer functions · Circuit construct · Construction graph · Protocol · Read Quality Profile · Read Alignment · Raw Signal · Verify vs Reference · Chromosomal microarray · Variant calls · Small molecule