✏️ A versatile DNA sequence optimizer
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May 10, 2025 - Python
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codon-optimization
Here are 22 public repositories matching this topic...
CodonTransformer (1M+ 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
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Jul 27, 2025 - Python
RNN-based Codon Optimization Tool. Publication: https://doi.org/10.1186/s12859-023-05246-8
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Apr 10, 2023 - Python
📊 Codon usage tables in code-friendly format + Python bindings
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May 9, 2025 - Python
A Go 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
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Jun 25, 2025 - Go
AI-assisted development MCP providing long-term, on-device "AI memory" for IDEs. Powered by Kuzu GraphDB and exposed via MCP server
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Aug 2, 2025 - Python
Cho codon optimization WIP
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Oct 20, 2024 - Jupyter Notebook
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
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Apr 13, 2021 - Python
Trias: an encoder-decoder model for generating synthetic eukaryotic mRNA sequences
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Jul 9, 2025 - Jupyter Notebook
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)
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Apr 8, 2021 - Python
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.
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Aug 12, 2022 - R
CUBseq analyses codon usage bias from RNA-seq data, producing robust CUB estimates that account for variants transcriptome-wide and in highly expressed genes.
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Mar 29, 2024 - R
A Novel Approach to Codon Optimization Based on Machine Learning and Genetic Algorithm
machine-learning bioinformatics genetic-algorithm bioinformatics-tool codon-optimization codon-usage
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Apr 2, 2023 - Jupyter Notebook
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
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Aug 1, 2025 - R
Phage library sequence generator with degenerate basepairs.
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Mar 14, 2023 - Python
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
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Sep 2, 2025 - Python
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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Sep 15, 2025 - Python
SIRIUS is a synthetic biology tool that, given a peptide sequence, designs n maximally divergent gene sequences
synthetic-biology linear-programming combinatorial-optimization mixed-integer-programming codon-optimization gene-design synonymous-codons
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Aug 26, 2025 - C++
It is simple codon optimiser by using codon bias and usage
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Mar 26, 2023 - Python
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