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Updated: Jan 13, 2026

Genomic MRI - a Public Resource for Studying Sequence Patterns within Genomic DNA

Genomic MRI - a Public Resource for Studying Sequence Patterns within Genomic DNA

Published on: May 9, 2011

Z-GENIE: a user-friendly R/Shiny resource for predicting Z-DNA forming regions in DNA.

Angel Garza Reyna¹, Melany Fuentes², David S Pisetsky^3,4,5

¹Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC 27705, USA. aig9@duke.edu.

|October 28, 2025

Summary

This summary is machine-generated.

Z-GENIE is a new tool that makes it easier to analyze Z-DNA, a left-handed DNA structure involved in health and disease. This graphical user interface automates complex processes, enabling broader research into Z-DNA's functions.

Keywords:

GUI Sequence motifs Shiny application Z-DNA genomic data visualization Z-GENIE Z-Hunt

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Published on: February 17, 2023

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Z-DNA is a left-handed DNA conformation with a zigzag backbone.
Its formation is influenced by base composition, modifications, and environmental factors.
Z-DNA plays roles in both normal physiology and disease, despite being energetically unfavorable.

Purpose of the Study:

To develop a user-friendly tool for predicting and analyzing Z-DNA potential across genomes.
To overcome the limitations of existing command-line tools like Z-Hunt for broader accessibility.
To facilitate the exploration of Z-DNA's involvement in biological processes and diseases.

Main Methods:

Introduction of Z-GENIE, an R/Shiny graphical user interface (GUI).
Z-GENIE automates the execution of the Z-Hunt algorithm and processes its output.
The tool accepts FASTA files, NCBI accession IDs, or manual sequences, generating CSV and BED summaries.

Main Results:

Z-GENIE provides interactive visualizations and outputs compatible with genomic browsers.
Performance benchmarks show rapid analysis for small to medium genomes (<20 Mb) and efficient parsing/export for large genomes (>50 Mb).
Case studies demonstrated Z-GENIE's ability to reproduce known Z-scores, identify Z-DNA clusters, and complement experimental data (ZIP-Seq, CUT&Tag).

Conclusions:

Z-GENIE democratizes genome-wide Z-DNA analysis by providing an intuitive GUI and flexible outputs.
The tool's rapid performance and visualization capabilities enhance the exploration of Z-DNA's roles in health and disease.
Z-GENIE broadens the accessibility of Z-DNA analysis for researchers without extensive coding expertise.