Codon-optimize protein sequences for expression via IDT's API, outputting JSON or FASTA.
npx skills add https://github.com/farnunglab/benchaid --skill codon-optimize
Please help me install this Agent Skill. Skill: codon-optimize Source: https://github.com/farnunglab/benchaid/tree/main/skills/codon-optimize Command: npx skills add https://github.com/farnunglab/benchaid --skill codon-optimize
Codon optimization automates translating protein sequences into DNA sequences optimized for expression in target hosts using IDT's API, reducing manual design time and error.
Provide a protein sequence or accession and run the codon optimization CLI to generate an IDT-optimized DNA sequence.
High-intent search queries and answers about installing and using this skill.
Codon optimization translates protein sequences into DNA sequences tailored for expression in a target host. This tool uses the IDT API to map raw amino acids or NCBI accessions to optimized DNA for hosts like E. coli, yeast, or mammalian cells.
Yes, you can optimize specific residues from an NCBI accession. Provide the accession via --accession and specify the desired region using the optional --residues flag to generate the corresponding optimized DNA sequence.
Yes, codon optimization supports insect, E. coli, mammalian, and yeast organisms. Specify your target expression host using the --organism flag, or let the tool infer it from your selected vector format.
Supported vector formats include 438, 1-, and pVEX. Specify your vector using the --vector flag, which also enables vector-based organism inference to tailor codon usage for cloning.
NVIDIA-BioNeMoPredict monomer protein structures from amino-acid sequences via OpenFold2 NIM microservices.
farnunglabDesign primers for LIC cloning, Gibson/HiFi assembly, and sequencing from NCBI accessions or raw sequences.
Runchuan-BUAnalyzes nucleotide and protein sequences for GC content, ORFs, restriction sites, and primers.
cultivariumOptimize DNA sequences for codon usage in a target host.
