✏️ A versatile DNA sequence optimizer
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Nov 5, 2025 - Python
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codon-optimizationHere are 38 public repositories matching this topic...Language: All
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CodonTransformer (2M+ Downloads); The tool for codon optimization, optimizing DNA for protein expression
machine-learning bioinformatics deep-learning synthetic-biology computational-biology gene-expression biotechnology codon-optimization codon codon-optimizer
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.
go bioinformatics synthetic-biology computational-biology sam genbank fasta fastq molecular-biology synbio rna-folding goldengate dna-barcode plasmids codon-optimization codon-usage pileup genetic-engineering dna-folding
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.
protein-sequences dna-sequences codons codon-optimization codon-usage codon-bias codon-frequencies codon-optimizer
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.
synthetic-biology cds pytorch dna language-model codon-optimization codon pytorch-lightning mrna-stability protein-language-model mrna-editing mrna-degradation mrna-translation-efficiency mrna-design codon-language-models mrna-sequences
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.
python bioinformatics synthetic-biology golden-gate codon-optimization moclo agrobacterium nicotiana-benthamiana plant-expression
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.
bioinformatics genomics synthetic-biology information-theory markov-chains codon-optimization codon-usage-bias mrna-vaccines
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.
A Novel Approach to Codon Optimization Based on Machine Learning and Genetic Algorithm
machine-learning bioinformatics genetic-algorithm bioinformatics-tool codon-optimization codon-usage
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
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.
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