score_rbs
Score the ribosome-binding site already in front of a start codon: the Shine-Dalgarno hybridisation energy, the mRNA folding that competes with it, the spacing it implies, and the resulting relative initiation strength. This reads an existing 5'UTR — design_rbs writes a new one.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| mrna | No | the mRNA (or DNA) carrying the UTR and the CDS — leave unset to use the open record. | |
| _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. | |
| start_pos | Yes | 0-based position of the start codon's first base within `mrna`. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| dgMrna | Yes | folding energy of the mRNA window that competes with initiation | |
| dgTotal | Yes | total free energy of the initiation state (null when no Shine-Dalgarno could be placed) | |
| sdStart | Yes | 0-based position in `mrna` where the winning Shine-Dalgarno begins (null when none could be placed) | |
| spacing | Yes | bases between the Shine-Dalgarno and the start codon (null when no Shine-Dalgarno could be placed) | |
| dgHybrid | Yes | Shine-Dalgarno · anti-SD hybridisation energy (null when no Shine-Dalgarno could be placed) | |
| sdLength | Yes | length of that Shine-Dalgarno, in bases (null when no Shine-Dalgarno could be placed) | |
| structure | Yes | dot-bracket secondary structure of the folded initiation window (empty when the window is too short to fold) | |
| relStrength | Yes | relative initiation strength (higher = stronger) | |
| structureStart | Yes | 0-based position in `mrna` that the first character of `structure` sits on |