Lab tool / v0.4 / Codon optimization & binder design

Plasmid Optimizer

Optimize DNA or amino-acid sequences for bacterial expression. Generate novel peptides with PepMLM and tune novelty (top-k, temperature).

What it does

Designs DNA sequences for genes you intend to clone into a plasmid and express in bacteria. You provide a gene or protein, choose constraints, and receive a codon-optimized DNA sequence with a constraint report.

Pipeline

Host sets the codon table and sensible defaults. Design (optional) generates novel peptide binders against a target protein with PepMLM. Sequence is what you optimize. Constraints shape GC%, secondary structure, repeats, and restriction sites. Output is a lab-ready artifact you can copy, FASTA-export, or attach to a synthesis order.

Host organism · required first step Codon table e_coli_K12

Design — Novel peptide generation

Optional

PepMLM: target protein → novel peptide sequences predicted to bind.

Need to design a binder first? Open PepMLM ＋

Sequence — Gene or protein to optimize

The page's center of gravity. Paste an amino-acid or DNA sequence, or fetch from UniProt.

Fetch from UniProt

Sequence

Amino acid DNA

Constraints

Advanced

Defaults are sensible for the chosen host. Override only if you need to.

GC min

GC max

Window (bp)

Avoid secondary structure Avoid repeats

Restriction enzymes to avoid

~1s for typical sequences

→

Output — Optimized artifact

No artifact yet

Run Optimize to generate a plasmid-ready DNA sequence and constraint report.