sirna_design

Active

declared in 1.1.0

Design siRNA duplexes against an mRNA target using the established Reynolds (2004) 8-criteria score and the Ui-Tei (2004) rules, plus a siDirect-style seed-duplex Tm off-target flag (≥21.5 °C). Returns ranked candidates with sense/guide oligos (with UU 3' overhangs) and, per candidate, a ready shRNA cassette (sense–loop–antisense–Pol III terminator). Heuristic sequence rules only — no RNA-folding accessibility model and no transcriptome-wide off-target search.

Parameters schema

{
  "type": "object",
  "required": [
    "target"
  ],
  "properties": {
    "target": {
      "type": "string",
      "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)."
    },
    "shRnaLoop": {
      "type": "string",
      "default": "TTCAAGAGA",
      "description": "Loop sequence used when assembling the shRNA cassette."
    },
    "minReynolds": {
      "type": "integer",
      "default": 6,
      "description": "Minimum Reynolds score (0–8) to keep; falls back to best-ranked if none qualify."
    }
  },
  "additionalProperties": false
}

What this tool wraps· 0 endpoints

min confidence0.70 0.50

No endpoints wrapped at confidence ≥ 0.50.

Parent server

com.seqbench/workbench

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