construct_autofix
ActiveTool of com.seqbench/workbench
declared in 1.1.0
Iteratively substitutes synonymous codons to resolve unwanted restriction sites (domestication for Golden Gate), homopolymers, tandem repeats, predicted secondary structure, cryptic RBS/polyA motifs and hidden alternate-frame ORFs that construct_qc flags — without changing the encoded protein (verified). Does NOT touch premature stops or GC extremes; re-run construct_qc afterward to confirm. A native TypeScript alternative to a constraint-solver sidecar.
Parameters schema
{
"type": "object",
"required": [
"sequence"
],
"properties": {
"gcLow": {
"type": "number",
"default": 30
},
"gcHigh": {
"type": "number",
"default": 70
},
"gcWindow": {
"type": "integer",
"default": 50
},
"organism": {
"enum": [
"ecoli",
"human",
"yeast",
"cho",
"pichia",
"insect",
"arabidopsis",
"zebrafish"
],
"type": "string",
"default": "ecoli",
"description": "Codon-usage table to prefer among synonymous options."
},
"sequence": {
"type": "string",
"description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)."
},
"maxPasses": {
"type": "integer",
"default": 3,
"description": "Repeat full passes until clean or no further progress."
},
"frameStart": {
"type": "integer",
"default": 1,
"description": "1-based nucleotide where the reading frame begins."
},
"avoidEnzymes": {
"type": "array",
"items": {
"type": "string"
},
"description": "Enzyme names whose internal sites should be removed (e.g. [\"BsaI\",\"BsmBI\"] for Golden Gate domestication)."
},
"homopolymerMin": {
"type": "integer",
"default": 8
},
"crypticOrfMinAa": {
"type": "integer",
"default": 20,
"description": "Minimum peptide length (aa) for a hidden alternate-frame ORF to be flagged."
}
},
"additionalProperties": false
}No endpoints wrapped at confidence ≥ 0.70.
Parent server
com.seqbench/workbench
1/7 registries