codon_optimality
Read-only
Frequency of optimal codons (Fop, Ikemura 1981) for an in-frame CDS against a real codon-usage table: what share of its codons are the ones a highly-expressed gene in that host would use.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| host | No | one of the three codon-usage tables bundled with the app. Only applies when table is not given. | E. coli K-12 |
| table | No | a codon-usage table this project holds, BY NAME, as the Codon Usage panel lists it — any organism. Takes precedence over `host`. This is the way to pass a table you fetched or built; `host` is only the three tables bundled with the app. | |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| sequence | No | the coding sequence, in frame (a length that is not a multiple of 3 is refused with the reason). Leave it empty to score the open record. | |
| threshold | No | Ikemura's optimality cutoff: a codon counts as optimal at this share of its family's most-used codon. 0.8 is the convention, not a measurement, and the right value is host-dependent. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| fop | Yes | frequency of optimal codons, 0-1 | |
| report | Yes | the full readout, including which host table answered | |
| scored | Yes | codons that carried a call — stops and unevidenced families are excluded from both halves | |
| nonOptimal | Yes | how many codons are NOT optimal (the honest denominator beside fop) | |
| optimalCodons | Yes | size of the optimal set the reference defines |