{
  "annotation_id": "02f728f5-a7e7-4288-8a49-ab46704d1443",
  "date_created": "2026-03-02T18:01:30.965000Z",
  "date_modified": "2026-03-02T18:01:30.965000Z",
  "file_hash": "2979da4d48c33401feb6a4afcb4847ae03271fbc74df27615232bbcb86074f8c",
  "private": false,
  "record": {
    "abstract": "We describe a faster and more accurate algorithm for computing the\nstatistical mechanics of DNA denaturation according to the Poland-Scheraga\ntype. Nearest neighbor thermodynamics is included in a complete and general\nway. The algorithm represents an optimization with respect to algorithmic\ncomplexity of the partition function algorithm of Yeramian et al.: We reduce\nthe computation time for a base-pairing probability profile from O(N2) to O(N).\nThis speed-up comes in addition to the speed-up due to a multiexponential\napproximation of the loop entropy factor as introduced by Fixman and Freire.\nThe speed-up, however, is independent of the multiexponential approximation and\nreduces time from O(N3) to O(N2) in the exact case. In addition to calculating\nthe standard base-pairing probability profiles, we propose to use the algorithm\nto calculate various other probabilities (loops, helices, tails) for a more\ndirect view of the melting regions and their positions and sizes.",
    "arxiv_id": "q-bio/0401011",
    "authors": [
      "E. Tostesen",
      "F. Liu",
      "T. -K. Jenssen",
      "E. Hovig"
    ],
    "categories": [
      "q-bio.BM"
    ],
    "doi": "10.1002/bip.10495",
    "journal_ref": "Biopolymers, 70, 364-376 (2003)",
    "title": "Speed-Up of DNA Melting Algorithm with Complete Nearest Neighbor   Properties",
    "url": "https://arxiv.org/abs/q-bio/0401011"
  },
  "schema_id": "dorsal/arxiv",
  "source": {
    "execution_id": "d130b692-90b0-43f5-858f-568b2d1258ca",
    "id": "arXiv Dataset IDs",
    "type": "Model",
    "variant": "snapshot-2026-03-01",
    "version": "0.1.0"
  },
  "user_id": 1000002
}