design_expression_variants
The expression-design deliverable: several coding sequences for one protein, each variant following a different published strategy (maximise codon adaptation, match the host's codon usage, harmonise with the native host, or preserve the initiation region), each scored by an engine — CAI, GC, the folding energy of the Kudla -4..+37 initiation window, and rare codons. It returns the comparison rather than one answer, because the strategies disagree about what limits expression and the researcher picks. Refuses a frame-shifted CDS, an internal stop or a missing host table rather than optimising nonsense.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| cds | No | the coding sequence to redesign, in frame and start-codon first. Unset falls back to THE SELECTION, on the strand the selection or its matching annotation states, then to the whole open record. | |
| seed | No | seed for the solver's random draws, so a listed variant can be regenerated exactly. Advanced. | |
| _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. | |
| gc_max | No | maximum GC fraction (0-1); set with gc_min. Advanced. | |
| gc_min | No | minimum GC fraction (0-1); set with gc_max. Advanced. | |
| feature | No | redesign this annotated CDS or gene by NAME instead of the selection, exactly as `codon_usage_analysis` takes one. Its own strand is used. Takes precedence over the selection; `cds` still wins over both. | |
| _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. | |
| postures | Yes | which strategies to design, in order. max_cai = every amino acid takes the target host's single most-used codon; match_usage = reproduce the target host's synonymous-codon distribution rather than its single best codon, so rare codons stay at their natural rate; harmonize = put each codon at the same relative adaptiveness it had in the gene's native host, so the elongation rhythm (and any pause the protein folds around) survives the transfer; native_initiation = leave nt +1…+37 of the coding sequence exactly as they are and match the host's codon usage only downstream, so the redesign cannot add secondary structure to the window Kudla found dominant. The set IS the deliverable — asking for one gets one, and there is no hidden default of three. | |
| upstream | No | the bases immediately 5' of the CDS (the 5'UTR/RBS region). Kudla's window starts 4 nt BEFORE the start codon, so without this the folding energy is reported over a truncated window and says so. | |
| gc_window | No | window in bp the GC bounds apply over (whole sequence when unset). Advanced. | |
| host_table | No | the TARGET host's codon-usage table, BY NAME, as the Codon Usage panel lists it. This is the way to pass a table: it resolves against the tables loaded in this project, so the numbers come from a table someone built or fetched. Leave unset and the active table is used. | |
| rare_below | No | within-family frequency below which a codon counts as RARE, for the report only — it adds no constraint. Omit and no rare-codon count is reported, which is the honest answer: "rare" has no host-independent definition. | |
| native_table | No | the gene's NATIVE host codon table, BY NAME from this project's loaded tables — required only for the `harmonize` posture, which matches relative adaptiveness BETWEEN two hosts. It must be a DIFFERENT table from `host_table`: harmonising a host against itself is a difference of zero. | |
| genetic_table | No | genetic code for the translation constraint (default Standard). Advanced. | Standard |
| avoid_patterns | No | literal patterns (restriction sites, homopolymers) every variant must not contain. | |
| host_table_tsv | No | ONLY for a table you are pasting yourself, measured elsewhere — prefer `host_table`, which names one this project already has. Do NOT write a table out from memory: codon frequencies are measured data, and a typed one is indistinguishable from a real one in the result. TSV: codon<TAB>count. Advanced. | |
| host_table_name | No | how to name that table on every score it produced (e.g. "E. coli K-12, Kazusa"), so a reported CAI is attributable. | |
| native_table_tsv | No | ONLY for a native table you are pasting yourself — prefer `native_table`. Do not write one out from memory (see `host_table_tsv`). TSV: codon<TAB>count. Advanced. |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| region | Yes | what was actually redesigned — the selection when there is one, otherwise the whole open record, naming the STRAND and where it came from. Empty when the caller passed `cds` outright, because then there is no region, only a sequence they named | |
| report | Yes | the whole comparison as Markdown — table, what each design trades, the provenance of every number, and the sequences — so it survives outside the transcript | |
| protein | Yes | the protein every variant encodes — asserted per variant, not assumed | |
| records | Yes | the variants as sequence RECORDS, so the run leaves the user holding the designs it describes | |
| skipped | Yes | postures that were asked for and could not run, each with the reason | |
| best_cai | Yes | the posture reaching the highest CAI — a ranking on ONE axis, never a recommendation | |
| distinct | Yes | how many of the variants are DIFFERENT sequences | |
| variants | Yes | one entry per posture: its sequence, what it was optimising for, what it trades away, and every score with the engine that produced it | |
| least_structured | Yes | the posture whose initiation window folds least tightly (the highest, least-negative dG) |