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.

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

Cho codon optimization WIP

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

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.

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.

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

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

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.

Phage library sequence generator with degenerate basepairs.

A script for codon harmonization.