Codon usage

CAI analyzer

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.

post/codon_adaptation_index

Request

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

Request body

sequencestring required

Coding sequence (DNA/RNA; should start in-frame at ATG).

organism'ecoli' | 'human' | 'yeast' | 'cho' | 'pichia' | 'insect' | 'arabidopsis' | 'zebrafish'
frameStartinteger

1-based position to start reading codons.

rareThresholdnumber

Relative adaptiveness (w) below this flags a codon as rare.

minRareRuninteger

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

Tool ran successfully.

okunknown required
toolstring required

The tool slug that ran.

resultobject required

Tool-specific output object. Its shape depends on the tool — call GET /{tool} or see the docs for each tool's fields.

Example response

{
  "provenance": {
    "apiVersion": "1.1.0"
  }
}

Changes

No recorded changes to this operation across all 1 revision of this API.