Getting started

PlasmidPop is a DNA sequence editor and plasmid viewer that runs entirely in your browser. There is no account and nothing is uploaded: files you open stay on your computer, and analysis runs on your own machine. The one request the editor makes to anyone else is Open from NCBI…, when you ask it to, and that sends NCBI the accession numbers you typed and nothing else.

PlasmidPop is free and open source under the MIT licence; the source is on GitHub.

Open something

Any of these gets you a sequence on screen:

• Drop a file anywhere on the page. GenBank, GenPept, FASTA, SnapGene .dna, .prot and .rna, AB1 and FASTQ files are recognised by their content, so the extension does not matter much. (A file dropped on the Align box or the enzyme import is read there instead of opening a tab.)
• Open file in the toolbar (or File ▸ Open file… once a document is open) shows the usual file picker.
• Paste (Ctrl+V) a GenBank record, a FASTA record, bare bases or bare protein residues while nothing is open. A record opens as such; bare letters become a new untitled sequence, DNA or protein as they read.
• New asks for the new sequence's Name and whether it is Linear, Circular or a Protein, then opens it empty with the cursor placed, so you can type straight away. Enter takes "Untitled" and the topology you chose last; Escape opens nothing.
• From NCBI… in the toolbar (or File ▸ Open from NCBI…) fetches a GenBank record by its accession number, such as L09137, or a protein's GenPept record, such as NP_000509; see Opening a record from NCBI.
• Open example loads pBR322 (4,361 bp, circular) to look around. On a phone it is the open pBR322 link on the start screen.

Each document opens in its own tab under the toolbar, so several can be open at once; the Files tab is the start screen. Files opened earlier appear there under Recent files, where they can be reopened, renamed or removed. See Files and storage.

What is on the screen

• Toolbar (top): the logo, the document name (click it to rename), its length and topology, then the File menu, Undo / Redo with the history list, the view switcher (Sequence, Map, Both), the Complement, Translations and Cut sites toggles, the Format and Edits menus, and the ? button that opens this guide.
• Document tabs (under the toolbar): Files, the Bench, then one tab per open document, and + for a new one. Tabs can be dragged into another order.
• Edit bar (under the tabs): Add feature, Delete selection, Reverse complement, Set origin here, Make circular / linear, Find.
• Views: the circular map on the left and the linear sequence view on the right. Both show the same selection and the same features.
• Sidebar (right): tabs for Features, ORFs, Translate, Primers, Enzymes, Cloning, Align and History (and Protein in front of a protein), in a narrow rail down the right-hand edge, each an icon above its label turned on its side. On a narrow window the rail becomes a row of tabs above the panel. From the keyboard the rail is one Tab stop: the arrow keys move along it and open the tab they reach, Home and End go to either end, and Alt+[ / Alt+] do the same from anywhere.
• Status bar (bottom): what is selected, warnings raised while opening the file, and the file name.

A dot after the document name (and on its tab) means the document has changed since you last downloaded it. Nothing is lost if you leave the page with the dot showing: every open document is written to this browser as you work and comes back when you return.

On a phone the screen is arranged differently: one pane at a time and no editing controls. See On a phone.

A two-minute tour

1. Click Open example.
2. In the Features tab click _tet_: the map and the sequence view jump to it and the selection is reported in the status bar.
3. Open the Enzymes tab. Enzymes that cut exactly once are ticked, and their cut sites are drawn on both views. Tick _EcoRI_ if it is not already.
4. Press Ctrl+F, type GAATTC and press Enter to step through the matches on either strand.
5. Click anywhere in the sequence view, type a few bases, and watch the features move with them. Ctrl+Z undoes it, and the History tab lists what you did.
6. Press Ctrl+S to download the result as a GenBank file.

Where your data lives

Open documents are written to the browser's local storage half a second after every change, and the tabs you had open come back when you return. That storage is per browser and per device. PlasmidPop never writes to a file on your disk: to get one, download it (Ctrl+S). Your sequences never leave your device (Open from NCBI sends NCBI an accession, not a sequence); the public build only counts anonymous feature usage (see the usage statistics section of the files page).

PlasmidPop can be installed as an app from the browser's address bar. Once installed it works offline, and .gb, .fa and .dna files can be opened with it from the file manager.

Citing PlasmidPop

If PlasmidPop helped with work you publish, please cite it as:

Usaj, M. PlasmidPop. Zenodo. doi:10.5281/zenodo.22907552

That DOI covers every version. The Zenodo record also lists a DOI for each release, for a methods section that names the exact version used. The version you are running is at the top of this guide, beside its title.