Z-Hunt-DP: accelerating thermodynamic Z-DNA prediction with dynamic programming
- 1Brock University
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.
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BibTeX
@misc{jumaily2026zhuntdp,
title = {{Z-Hunt-DP: accelerating thermodynamic Z-DNA prediction with dynamic programming}},
author = {M. Al Jumaily and H. Qureshi and H. Yan and Y. Li},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.14.751448},
url = {https://www.biorxiv.org/content/10.64898/2026.09.14.751448v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Z-Hunt-DP: accelerating thermodynamic Z-DNA prediction with dynamic programming
AU - M. Al Jumaily
AU - H. Qureshi
AU - H. Yan
AU - Y. Li
PY - 2026
DA - 2026/09/14
PB - bioRxiv
DO - 10.64898/2026.09.14.751448
UR - https://www.biorxiv.org/content/10.64898/2026.09.14.751448v1
AB - 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.
ER -