codon-optimization

✏️ A versatile DNA sequence optimizer

CodonTransformer (2M+ Downloads); The tool for codon optimization, optimizing DNA for protein expression

RNN-based Codon Optimization Tool. Publication: https://doi.org/10.1186/s12859-023-05246-8

📊 Codon usage tables in code-friendly format + Python bindings

A lua package for designing DNA.

AI-assisted development MCP providing long-term, on-device "AI memory" for IDEs. Powered by Kuzu GraphDB and exposed via MCP server

Trias: an encoder-decoder model for generating synthetic eukaryotic mRNA sequences

Cho codon optimization WIP

Simple Python program to perform codon optimization or heterology calculations.

Codonopt program is designed for codon optimization of protein sequences. The core of it based on the mathematical codon optimization proposed by Şen et al. (2020)

Codon language model disentangled from protein level semantics.

a decoder-only codon language model for codon optimization across all domains of life

Open-source CDS design and pre-synthesis sequence review for plant gene constructs.

Open-source verification suite & preprints on Medium-Range Conditional Codon Syntax (54 RefSeq taxa, 10 null models H0-H7) & the Double-Stranded Codon Torus T_4^3 = (Z/4Z)^3: Markov lumpability, antisense channel dominance (74-88%), TP53/RAS intron-exon splicing, JCVI-syn1.0/3.0, BNT162b2/mRNA-1273 duplex forensics & Duplex-Safe Viterbi compiler.

A tool to translate a given protein sequence into a DNA sequence based on a constructed codon use table for a target heterologous host, Nicotiana benthamiana.

Shiny Web app for automatic codon optimization based on codon usage in Strongyloides species, Pristionchus species, Brugia malayi, as well as user-provided custom codon lookup tables

A Novel Approach to Codon Optimization Based on Machine Learning and Genetic Algorithm

CUBseq analyses codon usage bias from RNA-seq data, producing robust CUB estimates that account for variants transcriptome-wide and in highly expressed genes.

A lightweight, research-focused tool for optimising virus codons to improve compatibility with a target mRNA vaccine, with rule-based amino-acid-preserving transformations and built-in sequence comparisons.

Recode a DNA sequence to match a target amino‑acid sequence with the minimal number of nucleotide changes, preserving the reading frame. Includes a CLI and Python API.