design_split_sites
Read-only
Decide where to CUT one sequence into Golden Gate fragments, optimising the split positions and the overhangs they create together.
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. | |
| traces | No | how many ranked alternatives to return. The best arrangement is rarely the only acceptable one, and the runner-up often avoids a site you care about. | |
| dataset | No | the measured ligation matrix to score against. OOGGA's own published choice is the T4 18 h 37 C set. Values: BsaI-HFv2 (BsaI-HFv2, Golden Gate cycling (4 nt)), BsmBI-v2 (BsmBI-v2, Golden Gate cycling (4 nt)), Esp3I (Esp3I, Golden Gate cycling (4 nt)), BbsI-HF (BbsI-HF, Golden Gate cycling (4 nt)), SapI (SapI, Golden Gate cycling (3 nt)), T4-01h-25C (T4 DNA ligase, 1 h at 25 C (4 nt)), T4-01h-37C (T4 DNA ligase, 1 h at 37 C (4 nt)), T4-18h-25C (T4 DNA ligase, 18 h at 25 C (4 nt)), T4-18h-37C (T4 DNA ligase, 18 h at 37 C (4 nt)). Advanced. | T4-18h-37C |
| _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 sequence to fragment, in one piece. Leave it empty to fragment the open record. | |
| fragments | No | pin the number of fragments instead of letting the search choose. Leave empty to take whatever the length window allows. | |
| exclude_to | No | end of that span, exclusive. Only applies when exclude_from is set. Advanced. | |
| max_length | No | longest allowed fragment, in bases — the vendor's upper limit, or the length you can sequence in one read. | |
| min_length | No | shortest allowed fragment, in bases — usually what your synthesis vendor will accept. | |
| exclude_from | No | start of a span no cut may fall in — a feature you need kept intact. Use with exclude_to. Advanced. | |
| alien_overhangs | No | junctions already committed elsewhere in the assembly (a fixed vector's own ends), which this set must not collide with. Advanced. | |
| fidelity_weight | No | exponent on the running FIDELITY — raise it to favour junctions that ligate to the right partner rather than a mismatched one. Advanced. | |
| efficiency_weight | No | exponent on the running ligation EFFICIENCY — raise it to favour junctions that ligate readily. Efficiency and fidelity are different failure modes: a junction can ligate eagerly and promiscuously. Advanced. | |
| max_overhang_identity | No | most positions two overhangs in the set may share before they are treated as confusable. Lower is stricter and rules out more arrangements. Advanced. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| score | Yes | the objective for the winning arrangement: net efficiency^w x net fidelity^w | |
| breaks | Yes | the winning arrangement's cut positions, in reading order | |
| report | Yes | the whole result, every arrangement in full | |
| dataset | Yes | the measured matrix actually scored against | |
| fragments | Yes | the fragments to order: sequence, span, length and the overhang at each end. Consecutive fragments overlap by exactly the four-base junction | |
| overhangs | Yes | the junctions the winning arrangement creates — wire this straight into score_overhang_fidelity to grade the set it chose | |
| candidates | Yes | how many arrangements were feasible at all under these constraints | |
| alternatives | Yes | the other ranked arrangements, each with its own breaks, score and junctions — the best is rarely the only acceptable one | |
| net_fidelity | Yes | net fidelity across every junction, 0-1 | |
| fragment_count | Yes | how many fragments the winning arrangement needs | |
| net_efficiency | Yes | net ligation efficiency across every junction, 0-1 |