scan_intrinsic_terminators
Find rho-independent (intrinsic) transcription terminators in a bacterial sequence: a stem-loop followed by a thymine-rich tail, scored by TransTermHP's published model (Kingsford, Ayanbule & Salzberg 2007). TWO NUMBERS, BOTH LOWER IS STRONGER - how well the hairpin folds and how thymine-rich the tail is - and NEITHER IS A FREE ENERGY: they are costs in this model's own scheme and must not be compared with a promoter's ΔG or a Turner ΔG. This is the question behind a downstream gene in an operon that goes quiet: a cryptic terminator inside an insert stops transcription that was meant to continue. Rho-DEPENDENT termination needs the protein and is not a sequence motif this or any such model can see. Reports every candidate clearing the two published cutoffs; TransTermHP itself lists one per position after its own overlap filters, so it reports fewer for the same sequence - a difference in reporting, not in scoring. No confidence value is given: TransTermHP's is a lookup into a table calibrated by its own GPL tooling, which is not shipped rather than approximated.
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. | |
| _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, best hairpin first. Advanced. | |
| both_strands | No | scan the reverse strand too. On by default: a terminator on the strand you did not draw still stops transcription that runs into it. | |
| 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
| Name | Required | Description | Default |
|---|---|---|---|
| count | Yes | how many are reported | |
| 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 | |
| strongest | Yes | the best-folding candidate, or null when none cleared both cutoffs | |
| terminators | Yes | the candidates, best hairpin first, each with its stem-loop, its tail, the stem length and both scores | |
| strongestHairpin | Yes | that candidate's hairpin score on its own, for a threshold downstream (lower is stronger). null when none cleared both cutoffs: there is no hairpin to score, and a 0 would pass a threshold as a measured value |