Phobius

A combined transmembrane topology and signal peptide predictor

API

A JSON endpoint for scripting. Interactive documentation is at /docs.

POST /api/predict

curl -s https://phobius.sbc.su.se/api/predict \
  -H 'Content-Type: application/json' \
  -d '{"sequence": ">my_protein\nMYGKIIFVLLLSAIVSISASSTTGVAMHTS..."}'

Response:

{
  "predictions": [
    {
      "id": "my_protein",
      "length": 150,
      "transmembrane_count": 1,
      "signal_peptide": true,
      "cleavage_site": 19,
      "topology": "n5-15c19/20o92-114i",
      "features": [
        {"label": "n", "start": 1,  "stop": 4},
        {"label": "h", "start": 5,  "stop": 15},
        {"label": "c", "start": 16, "stop": 19},
        {"label": "C", "start": 20, "stop": 20},
        {"label": "o", "start": 21, "stop": 91},
        {"label": "M", "start": 92, "stop": 114},
        {"label": "i", "start": 115,"stop": 150}
      ]
    }
  ]
}

Pass "plot": true to receive an SVG posterior plot per sequence in an svg field. Limits are the same as the web form: 100 sequences and 50,000 residues per request.

Plain text

POST /api/predict.txt with the same body returns the long feature-table format as text/plain; add ?format=short for the one-line-per-protein format.