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Updated: May 26, 2025

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ZSeeker: An optimized algorithm for Z-DNA detection in genomic sequences.

Guliang Wang1, Ioannis Mouratidis2,3, Kimonas Provatas3

  • 1Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, Austin, TX, USA.

Biorxiv : the Preprint Server for Biology
|February 24, 2025
PubMed
Summary

Z-DNA, a left-handed DNA form, is linked to genetic instability. ZSeeker is a new computational tool that accurately detects Z-DNA forming sequences in genomes, aiding disease research.

Keywords:
Z-DNAalgorithm designsearch toolweb interface

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Z-DNA is an alternative left-handed DNA helix with a zigzag backbone, distinct from B-DNA.
  • Z-DNA is implicated in crucial biological processes like transcription, replication, and DNA repair, and can cause genetic instability.
  • Repetitive purine-pyrimidine sequences are known to potentially form Z-DNA structures.

Purpose of the Study:

  • To develop a novel computational tool, ZSeeker, for accurate detection of Z-DNA forming sequences.
  • To address limitations of existing methods for Z-DNA sequence identification.
  • To provide an accessible and user-friendly platform for analyzing Z-DNA potential in genomic data.

Main Methods:

  • Developed ZSeeker, a computational tool utilizing a novel methodology informed by experimental data.
  • Implemented ZSeeker as a standalone Python package and a web interface.
  • Enabled users to input genomic sequences, adjust parameters, and visualize Z-DNA distributions and Z-scores.

Main Results:

  • ZSeeker achieves refined detection of potential Z-DNA forming sequences.
  • The tool offers efficient, high-throughput analysis with enhanced accuracy.
  • Provides downloadable visualizations of Z-DNA sequence distributions and Z-scores.

Conclusions:

  • ZSeeker facilitates accurate identification of Z-DNA forming sequences across genomes.
  • The tool's accessibility and customizability support broad research applications.
  • ZSeeker has the potential to advance understanding of Z-DNA's role in cellular functions, genetic instability, and human diseases.