{
  "annotation_id": "954aaa3c-1ed8-4749-942e-a13e2be45d3f",
  "date_created": "2026-03-02T18:01:21.294000Z",
  "date_modified": "2026-03-02T18:01:21.294000Z",
  "file_hash": "d524bee572361ac167c0902f92410bb90e6a414a1bd799b14c72167e74899bbb",
  "private": false,
  "record": {
    "abstract": "We describe a dynamic programming algorithm for predicting optimal RNA\nsecondary structure, including pseudoknots. The algorithm has a worst case\ncomplexity of ${\\cal O}(N^6)$ in time and ${\\cal O}(N^4)$ in storage. The\ndescription of the algorithm is complex, which led us to adopt a useful\ngraphical representation (Feynman diagrams) borrowed from quantum field theory.\nWe present an implementation of the algorithm that generates the optimal\nminimum energy structure for a single RNA sequence, using standard RNA folding\nthermodynamic parameters augmented by a few parameters describing the\nthermodynamic stability of pseudoknots. We demonstrate the properties of the\nalgorithm by using it to predict structures for several small pseudoknotted and\nnon-pseudoknotted RNAs. Although the time and memory demands of the algorithm\nare steep, we believe this is the first algorithm to be able to fold optimal\n(minimum energy) pseudoknotted RNAs with the accepted RNA thermodynamic model.",
    "arxiv_id": "physics/9807048",
    "authors": [
      "Elena Rivas",
      "Sean R. Eddy"
    ],
    "categories": [
      "physics.bio-ph",
      "q-bio"
    ],
    "title": "A dynamic programming algorithm for RNA structure prediction including   pseudoknots",
    "url": "https://arxiv.org/abs/physics/9807048"
  },
  "schema_id": "dorsal/arxiv",
  "source": {
    "execution_id": "169daf92-2828-4ab1-bb1c-d4a937d4bd15",
    "id": "arXiv Dataset IDs",
    "type": "Model",
    "variant": "snapshot-2026-03-01",
    "version": "0.1.0"
  },
  "user_id": 1000002
}