---
title: "CAI analyzer"
method: POST
path: "/codon_adaptation_index"
tags: ["Codon usage"]
---

# CAI analyzer

`POST /codon_adaptation_index`

## Request

- Base URL: `https://seqbench.com/api/v1`
- URL: `https://seqbench.com/api/v1/codon_adaptation_index`
- Auth: none required

Codon Adaptation Index (CAI) and per-codon relative adaptiveness of a CDS against an expression host, with rare-codon and GC3 analysis.

Batchable via `POST /batch`.

## Request body

- object
  - `sequence` string, required: Coding sequence (DNA/RNA; should start in-frame at ATG).
  - `organism` 'ecoli' | 'human' | 'yeast' | 'cho' | 'pichia' | 'insect' | 'arabidopsis' | 'zebrafish'
  - `frameStart` integer: 1-based position to start reading codons.
  - `rareThreshold` number: Relative adaptiveness (w) below this flags a codon as rare.
  - `minRareRun` integer: Shortest stretch of CONSECUTIVE rare codons to report as a run. A CAI is a geometric mean, so fifteen rare codons scattered singly and the same fifteen in three runs of five score alike and carry the same rareCount; only the runs say where they are clustered.

## Response `200`

Tool ran successfully.

- SuccessResponse: Standard success envelope returned by every single-tool call.
  - `ok` unknown, required
  - `tool` string, required: The tool slug that ran.
  - `result` object, required: Tool-specific output object. Its shape depends on the tool — call `GET /{tool}` or see the docs for each tool's fields.
  - `gate` GateResult
    - `pass` boolean, required: True if and only if every hard check passed.
    - `checks` GateCheck[], required
      - `id` string, required
      - `label` string, required
      - `severity` 'hard' | 'soft', required
      - `pass` boolean, required
      - `message` string, required
      - `value` number
      - `threshold` string
    - `notChecked` string[], required: Honest list of what this gate does NOT verify.
  - `provenance` Provenance, required
    - `apiVersion` string, required
    - `tool` union, required: Tool slug, or an array of slugs (one per step) for a workflow.
      - string
      - string[]
    - `generatedAt` string, date-time, required: ISO 8601 timestamp of when the result was generated.

## Other responses

- `400`: Invalid argument or the tool could not run.
- `404`: Unknown tool.
- `429`: Rate limited (metered tools only). Body carries code `rate_limited` and retryable `true`; honor the Retry-After header.
- `503`: A metered tool is momentarily at capacity. The identical request should succeed after Retry-After; body carries code `upstream_unavailable`.

---

[API](https://skmtc.dev/seqbench/apis/seqbench-api.md) · [All operations](https://skmtc.dev/seqbench/apis/seqbench-api/llms.txt) · [OpenAPI document](https://skmtc.dev/seqbench/apis/seqbench-api/revisions/132575216865?raw)