codon_usage_distance
Read-only
How this region's codon usage compares with the record's OTHER genes (CUFS, Diament, Pinter & Tuller 2014).
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| _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. | |
| feature | No | score this annotated CDS or gene by NAME instead of the selection (the panel's "A CDS / feature…" mode). Its own strand is used unless `reverse` says otherwise. | |
| reverse | No | read the region as the reverse complement. Leave unset to take the strand from the annotation when the selection is exactly an annotated CDS or gene, which is what the panel does. | |
| _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. | |
| synonymous | No | normalise each amino acid's codons to sum to 1 (synCUFS), so what remains is the synonymous choice alone. Off compares all 64 codon frequencies, which also reflects amino-acid composition. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| region | Yes | what was actually scored, naming the STRAND and where it came from — a reverse-strand gene read forwards is a wrong answer, not a missing one | |
| ceiling | Yes | the largest distance this run could have produced, for the mode it ran in — read a distance against THIS, never against a constant | |
| nearest | Yes | the feature whose codon usage is closest to the scored region | |
| skipped | Yes | features that were NOT compared and why — a feature too short for the statistic is reported, never dropped | |
| compared | Yes | how many features were compared | |
| furthest | Yes | the feature whose codon usage is least like the scored region — the odd one out | |
| neighbours | Yes | every other coding feature with its CUFS distance, nearest first — name, span, codons compared and distance | |
| synonymous | Yes | whether amino-acid composition was normalised away — the same column of figures means a different thing under each | |
| strandSource | Yes | `explicit` (you passed `reverse`), `feature` (taken from the annotation the selection matches) or `default` (forwards, nothing said otherwise) | |
| nearestDistance | Yes | its distance. 0 would mean an identical codon distribution; the maximum depends on the mode and is reported as `ceiling` beside it — sqrt(2 ln 2) = 1.177 for the plain form, sqrt(2 ln 2 F) = 5.396 for the synonymous one, which normalises each amino acid separately |