Which organisms can I analyse against?

Hosts are resolved from a real codon usage database by name, so the set is not a short built-in list. Where a cached subset is used, the page states what it covers.

What is the codon adaptation index?

A single number summarising how closely a coding sequence matches the codon preferences of a host, computed from that host codon usage table.

Analyze · experimental

Codon Usage Analysis

Read the codon composition of a coding sequence against a host: which codons are rare in that host, what the codon adaptation index comes to, and how the start and stop context looks. Host tables come from a real codon usage database rather than a table typed into the source.

Open Codon Usage Analysis 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

01Codon adaptation index against a selected expression host
02Per-codon usage matrix for the sequence
03Rare-codon identification, including runs that stall translation
04GC content overall and by codon position
05Start and stop codon usage readouts
06N-end rule readout for the encoded protein
07Host selection by organism name, resolved against real codon usage data

What it runs on

Codon statistics run on the pydna and DnaChisel ports; host codon usage comes from the Kazusa codon usage database rather than from tables embedded in the source (CLAUDE.md §1b). The panel runs on @ports/codon, @ports/protein.

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

Which organisms can I analyse against?: Hosts are resolved from a real codon usage database by name, so the set is not a short built-in list. Where a cached subset is used, the page states what it covers.
What is the codon adaptation index?: A single number summarising how closely a coding sequence matches the codon preferences of a host, computed from that host codon usage table.

Also searched as

codon usage analysis online · codon adaptation index calculator · CAI calculator · rare codon finder · codon usage table lookup · GC3 content calculator · codon frequency analysis · codon bias analysis online · rare codon cluster finder · Kazusa codon usage alternative · is my gene codon optimized