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CloneIt

CloneIt is a plasmid map editor aligned with common web / Angular-style plasmid layouts — circular and linear topology, rich annotations, sequence inspection, restriction analysis, TFBS scans, primer overlays, and project export. Summarized below from CloneIt_Key_Features.txt with representative screenshots from version 0.9.

Key features

Plasmid maps

Circular and linear topology with a customizable main track (radius, ticks, numbering, optional double track).
Manual features with start/end, name, color, strand (+ / − / neutral); draggable on the map.
Style presets and saved styles; optional center label, text boxes with connectors.
Zoom, pan, and arc selection for regions of interest.

Sequences & import

Load DNA from FASTA, plain text, GenBank (NCBI fetch), SnapGene (.dna), and CloneIt / JSON projects.
Auto-detect features using FASTA reference libraries; sequence length sets scale with topology.

DNA sequence viewer

Multi-line and single-line arc views; optional antisense; 5′ / 3′ labels.
Translation with auto-frame (ATG-based ORF) or fixed frame; search highlighting and optional mutation markers.
Monospace-aligned base numbering.

Restriction enzymes

Sites from a pattern library (CSV / bundled MCS); mapped on plasmid and sequence views.
Cut positions shown between bases in multi-line mode.

TFBS (transcription factor binding sites)

PWM scan against bundled MEME-format motif libraries.
Adjustable score threshold and hit limits.

PCR primers

Primer library (database + CSV) with UI search and editing.
Search primer sequences against the construct and overlay hits as features.

Sequence alignments

Ingest alignments from the companion sequence aligner (or API); trace-friendly viewer.
Store alignments inside the project history.

Plasmid library (optional)

Index folders of .json / .cloneit projects; search by metadata or DNA substring.

Export & project

Export maps as SVG or JPG.
Save/load CloneIt-compatible JSON projects.
Shippable Windows .exe / installer builds — PyInstaller-packaged; no Python install needed for packaged users.

Technical note

Runs locally in the browser (for example http://127.0.0.1:8080) backed by a small Flask server started via app.py or the packaged executable.

Screenshots

CloneIt 0.9 combines circular maps, arc-aware sequence lanes (single-line mode shown below), TFBS tables with CSV export, primer tooling, and restriction overlays — illustrated across several constructs such as pNL1.2[NlucP] (3233 bp).

CloneIt 0.9 main interface showing TFBS hits panel, single-line DNA arc view with coloured motifs and restriction site NheI, and circular plasmid backdrop. — Main workspace: TFBS hits browser with filtering/export, arc-aligned sequence viewer with motif overlays (including restriction markers such as NheI), and circular map preview — illustrating TF scanning plus coupled sequence/map UX.

Circular plasmid map with labelled restriction enzymes around pNL1.2 NlucP backbone. — Circular map emphasizing MCS-rich clusters of restriction enzymes, ori/AmpR selection cassette spacing, and polyadenylation signals for cloning QC review.

CloneIt circular plasmid showing NanoLuc hPEST SV40 poly-A ori AmpR annotations. — Alternate styling preset highlighting promoter/report genes (Nluc, hPEST), SV40 poly(A), high-copy origin, and ampicillin resistance trajectory along the backbone.

Circular map variant showing coloured pause site Nluc hPEST SV40 poly-A ori and AmpR segments. — Emphasizes directional transcription cues via wedge glyphs plus positional ticks — representative of CloneIt’s track customization / preset tooling described above.

Bundled documentation

Copy bundled alongside executable artifacts:

CloneIt_Key_Features.txt — authoritative checklist mirrored on this page.
CloneIt_User_Manual.docx — expanded HOWTO reference (same link as the banner above).
CloneIt-0.9-Setup.exe — Windows installer package (~31 MB); distribute under your lab IT policies only (same link as the installer tile above).