Why build from highly expressed genes?

Because a whole-genome table averages over genes that are barely transcribed. The ribosomal-protein subset is the standard proxy for the codon bias of a highly expressed gene, which is the bias a heterologous construct is usually optimised toward.

Do I need to be online?

No. Tables are built from a CDS FASTA you supply or a TSV you paste, entirely in the browser.

Can the table be used by the optimizer?

Yes. A table built or imported here is what the codon optimisation and codon usage analysis tools read.

Analyze · experimental

Codon Tables

A codon optimisation is only as good as the usage table behind it. Build one from a real CDS corpus, either whole-genome or from the highly expressed ribosomal-protein genes, or bring a table you already trust, and read it as the wall chart with usage on every codon.

Open Codon Tables Open the Codon usage sample

Thirteen real CDSs — yeast ADH1, ten mammalian expression parts (mTagBFP2 · PuroR ×2 · BSDR · Kozak-ATG · linker · IgK leader · L7Ae), the rare-codon-loaded ccdB cassette, pBR322 for its reverse-strand bla and human EMX1 for a three-exon spliced CDS: compare CAI, GC and rare codons across hosts, and optimize a gene that runs the other way

What it does

01A usage table built from a genome CDS FASTA, whole-genome or from highly expressed ribosomal-protein genes
02Build statistics reported for the corpus the table came from
03A pasted or loaded codon-usage TSV imported as a table
04The genetic-code chart with per-codon usage percentages, in DNA or RNA spelling
05Tables exported as canonical TSV, and kept for the optimizer to use

What it runs on

Table building, TSV parsing and the chart all run on the golden-validated `@ports/codon` engine. Every table comes from a real CDS corpus or a real TSV you provide. The panel runs on @ports/codon, @ports/mutagenesis.

Everything runs client-side. Files are parsed in the browser and projects are saved on this machine, so an unpublished sequence is never uploaded.

Questions

Why build from highly expressed genes?: Because a whole-genome table averages over genes that are barely transcribed. The ribosomal-protein subset is the standard proxy for the codon bias of a highly expressed gene, which is the bias a heterologous construct is usually optimised toward.
Do I need to be online?: No. Tables are built from a CDS FASTA you supply or a TSV you paste, entirely in the browser.
Can the table be used by the optimizer?: Yes. A table built or imported here is what the codon optimisation and codon usage analysis tools read.

Also searched as

codon usage table · build codon usage table from genome · codon frequency table · genetic code chart with usage · highly expressed genes codon table · codon usage tsv · Kazusa codon usage database alternative · codon usage table from a FASTA file · RSCU calculator · relative synonymous codon usage