verify_assembly
ActiveTool of com.seqbench/workbench
declared in 1.1.0
Deterministic self-check: given the same method/parts cloning_simulate would use (restriction-ligation, Gibson, or Golden Gate — optionally deriving a part by in-silico PCR first), re-derive the expected WHOLE product and diff it against a claimed final sequence. Returns pass/fail plus the exact position and nature of any discrepancy — not an opinion, the same deterministic simulation SeqBench already runs, run a second time as a check. See verify_construct for a narrower, insert-only check that doesn't require declaring the vector/enzymes/method.
Parameters schema
{
"type": "object",
"required": [
"method",
"claimedConstruct"
],
"properties": {
"names": {
"type": "array",
"items": {
"type": "string"
},
"description": "Optional labels for each fragment."
},
"coding": {
"type": "boolean",
"default": false,
"description": "Report amino-acid effects of any mismatch, assuming claimedConstruct is (or contains) a coding sequence."
},
"enzyme": {
"type": "string",
"default": "BsaI",
"description": "Type IIS enzyme for Golden Gate."
},
"insert": {
"type": "string",
"description": "Insert sequence (restriction method). Omit if insertPcr is given."
},
"method": {
"enum": [
"restriction",
"gibson",
"goldengate"
],
"type": "string",
"description": "Assembly method used."
},
"vector": {
"type": "string",
"description": "Vector sequence (restriction method). Omit if vectorPcr is given."
},
"enzyme3": {
"type": "string",
"default": "BamHI",
"description": "3′ enzyme (restriction method)."
},
"enzyme5": {
"type": "string",
"default": "EcoRI",
"description": "5′ enzyme (restriction method)."
},
"circular": {
"type": "boolean",
"default": true,
"description": "Treat the product/claimed construct as circular (most plasmids are)."
},
"fragments": {
"type": "array",
"items": {
"type": "string"
},
"description": "Fragments (5′→3′), assembled head-to-tail (gibson/goldengate). Use \"\" as a placeholder for any fragment supplied instead via the matching fragmentPcrs[i]."
},
"insertPcr": {
"type": "object",
"description": "Derive the insert by PCR instead: {template, forwardPrimer, reversePrimer, maxMismatches?, circular?}."
},
"vectorPcr": {
"type": "object",
"description": "Derive the vector by PCR instead: {template, forwardPrimer, reversePrimer, maxMismatches?, circular?}."
},
"frameStart": {
"type": "integer",
"default": 1,
"description": "1-based reading-frame start on claimedConstruct, used when coding is true."
},
"overlapLen": {
"type": "integer",
"default": 20,
"description": "Gibson homology-arm length (bp)."
},
"armTmTarget": {
"type": "number",
"default": 60,
"description": "Target annealing Tm (°C) for primer arms."
},
"fragmentPcrs": {
"type": "array",
"items": {
"type": "object"
},
"description": "Parallel to fragments, same length: null (or omit) to use fragments[i] directly, or a PCR spec {template, forwardPrimer, reversePrimer, maxMismatches?, circular?} to derive that fragment instead."
},
"claimedConstruct": {
"type": "string",
"description": "The sequence you claim you ended up with."
}
},
"additionalProperties": false
}No endpoints wrapped at confidence ≥ 0.50.
Parent server
com.seqbench/workbench
1/7 registries