codon-optimization
There are 22 repositories under codon-optimization topic.
Edinburgh-Genome-Foundry/DnaChisel
:pencil2: A versatile DNA sequence optimizer
Adibvafa/CodonTransformer
CodonTransformer (1M+ Downloads); The tool for codon optimization, optimizing DNA for protein expression
Lattice-Automation/icor-codon-optimization
RNN-based Codon Optimization Tool. Publication: https://doi.org/10.1186/s12859-023-05246-8
Edinburgh-Genome-Foundry/python_codon_tables
:bar_chart: Codon usage tables in code-friendly format + Python bindings
Koeng101/dnadesign
A Go package for designing DNA.
elementalcollision/GraphMemory-IDE
AI-assisted development MCP providing long-term, on-device "AI memory" for IDEs. Powered by Kuzu GraphDB and exposed via MCP server
lareaulab/Trias
Trias: an encoder-decoder model for generating synthetic eukaryotic mRNA sequences
RJain12/choformer
Cho codon optimization WIP
tdseher/simple-codon-optimizer
Simple Python program to perform codon optimization or heterology calculations.
Maximato/Codonopt
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)
anchitaaghag/Codon-Optimization-for-Biopharming
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.
Gumgo91/CodonHumanization
A Novel Approach to Codon Optimization Based on Machine Learning and Genetic Algorithm
HallemLab/Wild_Worm_Codon_Adapter
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
stracquadaniolab/cubseq-nf
CUBseq analyses codon usage bias from RNA-seq data, producing robust CUB estimates that account for variants transcriptome-wide and in highly expressed genes.
Boehringer-Ingelheim/SynCodonLM
Codon language model disentangled from protein level semantics.
chaupka/codon_harmonization
A script for codon harmonization.
retospect/phagetrix
Phage library sequence generator with degenerate basepairs.
AmirUCR/SIRIUS
SIRIUS is a synthetic biology tool that, given a peptide sequence, designs n maximally divergent gene sequences
MPurushothamRao/Codon-Optimiser-by-codon-bias
It is simple codon optimiser by using codon bias and usage
xiongQvQ/codon-recoder
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.
abondrn/polymerust
RNA folding and codon optimization in pure Rust
EpicenterPrograms/codonoptimizer
A program which allows codon optimization for multiple species at the same time