scan_sigma70_promoters
Read-only
Find σ70 (housekeeping) promoters in a bacterial sequence and say how strong each one is, using the published La Fleur-Hossain-Salis biophysical model - six interaction motifs (UP element, -35, spacer, extended -10, -10, discriminator) plus the R-loop strength of the first transcribed bases, fitted on 22,132 characterised promoters. THE NUMBER IS A FREE ENERGY AND MORE NEGATIVE IS STRONGER, which is the opposite direction from a score; the transcription rate beside it is the paper's own rate law over that energy. It answers "could RNA polymerase start here", not "does it": nothing here knows about regulators, supercoiling or growth phase. It is E. coli σ70 and says nothing about σ38/σ32/σ54 promoters or about another organism's polymerase.
Input Schema
TableJSON 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. | |
| max_dg | No | report only configurations at or below this ΔG_total. UNSET BY DEFAULT and deliberately so: this model publishes no significance cutoff, so the answer is a RANKING of the strongest configurations rather than a set of calls, and inventing a floor here is the exact defect the scanner this replaces had. Set it when you have a threshold of your own. In kcal/mol. | |
| _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 DNA to scan - leave unset to use the open record. | |
| region_end | No | 0-based inclusive end. Unset = the whole sequence. Advanced. | |
| max_results | No | how many to return, strongest (most negative) first. Advanced. | |
| both_strands | No | scan the reverse strand too. On by default: a cryptic promoter does not care which strand your insert was drawn on, and scanning one is how one gets missed. | |
| region_start | No | 0-based inclusive start of the region to scan. Unset = the whole sequence; pass the selection's start to scope to it. Advanced. |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| count | Yes | how many are reported (`max_results`, or fewer if the sequence is short or `max_dg` was set) | |
| offset | Yes | where the scanned stretch starts in the sequence: add it to every position above for sequence coordinates. 0 unless a region was given | |
| promoters | Yes | the configurations, strongest (most negative) first, each with its six motif sequences, their positions and the per-motif energies that sum to its total | |
| strongest | Yes | the most negative ΔG_total, or null when the sequence is too short to hold one | |
| strongestDg | Yes | that hit's ΔG_total on its own, for a threshold downstream, or null when there is no hit |