Plasmid Editor: Cloning & AAV

Reborn Pharmaceuticals, LLC

About this app

Plasmid editor and viral vector design tool for molecular cloning. Import a plasmid and see every element checked against its own sequence, with how each call was established. Replace a promoter, add or remove a gene, or swap a part, and get a finished construct
1. IDENTIFY WHAT IS ACTUALLY THERE
Import a SnapGene, GenBank or FASTA file. Every element is matched against the bases rather than trusted from the label, and each one is marked with how it was established: confirmed by exact sequence match, taken from the file's own annotation, or predicted from structure alone. Where the file and the sequence disagree — an element annotated on the wrong strand, the same feature called twice at different boundaries - you are told.
The elements you can change are listed first. ITRs, the origin, the resistance marker and the recombinase sites are kept separate, because editing them gets you nothing back from the prep.
2. FOUR EDITS
Replace the promoter. Add a gene. Remove a gene. Swap a part.
Each one produces a finished construct, the Gibson assembly plan, and primers with melting temperatures. Homology arms extend until they are unique, so repeated sequence does not produce an ambiguous junction. Every design is re-assembled in silico before it is issued: if the product does not come back identical, you do not get the plan.
3. DESIGNS THAT WOULD HAVE FAILED QUIETLY
A cargo in a FLEX or DIO cassette is stored antisense. Paste a normally written coding sequence into those coordinates and it goes in backwards. The app works out the required orientation from the cassette architecture and places it correctly.
An annotated CDS is often only part of a longer reading frame. Replace just the annotated piece and your new gene inherits whatever sat in front of it - tags, targeting motifs, linkers - as an N-terminal fusion. The app reads upstream in frame, names what it finds, and offers to remove it.
4. PACKAGING SIZE, BEFORE YOU ORDER
The ITR-to-ITR genome is measured and compared against the real limit for AAV, self-complementary AAV, lentivirus or adenovirus. When a design is too large, you get specific reductions with the base pairs each one saves and what it costs you.
5. PROMOTERS AND CAPSIDS
Sixteen promoters covering neurons, astrocytes, hepatocytes, cardiomyocytes and ubiquitous expression. Each was read out of a publicly deposited plasmid map and carries the Addgene number and the exact coordinates it came from. They are exactly what that deposit contains — not sequence written from memory.
A capsid guide pairs cell types with AAV serotypes, each with the caveat that matters.
6. EXPORT
GenBank, SnapGene, or FASTA. Annotations, strands and topology survive the first two; FASTA is bases only, and the app says so before you pick it.
7. PRIVATE BY CONSTRUCTION
No account. No analytics. No advertising. Your vectors stay on your device. The app works offline; the one exception is an optional NCBI lookup when you type an accession, which sends nothing but that accession.
8. COMPANION APP
Gene Search, free, finds genes and accessions in NCBI and hands them straight to this app.
Plasmid Editor is a design aid. Every construct is a prediction from the sequence you supplied, and predictions can be wrong — most often because the file's own annotations were wrong. Verify every junction by sequencing before you rely on a construct.

What’s new

Import a plasmid and see every element checked against its own sequence, with how each call was established. Replace a promoter, add or remove a gene, or swap a part, and get a finished construct with Gibson primers and an in-silico re-assembly check. Packaged genome size is measured against the real limit for your vector system. Sixteen promoters, each traced to a deposited plasmid. Export to GenBank, SnapGene or FASTA. Works offline.