{
  "abstract": "Z-DNA is a left-handed DNA conformation implicated in gene regulation and chromatin dynamics. Because it is usually less thermodynamically favorable than canonical B-DNA under physiological conditions, computational tools are needed to identify sequences likely to adopt the Z conformation. Legacy Z-Hunt uses a dinucleotide thermodynamic model, but searches every anti/syn assignment in a window, causing its conformation search to grow exponentially with window size. We present Z-Hunt-DP, an exact dynamic programming reformulation that preserves the original thermodynamic objective while reducing this search from O(2^d) to O(d) for a window of d dinucleotide positions. On benchmark windows, Z-Hunt-DP matched the brute-force minimum energy within numerical tolerance and achieved a 3.30x10^5 speedup at 20 dinucleotides. In an interval-localization benchmark on public human loci with experimentally mapped Z-DNA, it recovered the clipped reference interval in all 24 cases and was the most stable localizer under midpoint-core and expanded-panel analyses. Since the comparison set mixes thermodynamic, heuristic, and learned models, these cross-tool results are interpreted as localization comparisons rather than direct thermodynamic score tests. The source code and benchmark materials are available at https://github.com/Aljumaily/Z-Hunt-DP.",
  "abstract_shown": true,
  "affiliations": [
    "Brock University"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 4,
  "authors": [
    {
      "name": "M. Al Jumaily"
    },
    {
      "name": "H. Qureshi"
    },
    {
      "name": "H. Yan"
    },
    {
      "affs": [
        0
      ],
      "name": "Y. Li"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/5c1aqtkqjaxqy.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.14.751448",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.14.751448v1.full",
  "id": "5c1aqtkqjaxqy",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.14.751448v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "bioinformatics"
    ],
    [
      "openalex",
      "1312|DNA and Nucleic Acid Chemistry"
    ]
  ],
  "openalex": "W7213945765",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.14.751448v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-14",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/5c1aqtkqjaxqy.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:23:26Z",
      "native_id": "10.64898/2026.09.14.751448",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.14.751448v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "Z-Hunt-DP: accelerating thermodynamic Z-DNA prediction with dynamic programming",
  "title_text": "Z-Hunt-DP: accelerating thermodynamic Z-DNA prediction with dynamic programming",
  "type": "preprint",
  "updated_at": "2026-10-30T12:23:26Z",
  "url": "https://research.draconitic.com/paper/5c1aqtkqjaxqy",
  "venue": "bioRxiv",
  "versions": []
}