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

Abstract Z-deoxyribonucleic acid (Z-DNA) is an alternative left-handed DNA structure with a zigzag-shaped backbone that differs from the right-handed canonical B-DNA helix. Z-DNA has been implicated in various biological processes, including transcription, replication, and DNA repair, and can induce...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Briefings in bioinformatics Jg. 26; H. 3
Hauptverfasser: Wang, Guliang, Mouratidis, Ioannis, Provatas, Kimonas, Chantzi, Nikol, Patsakis, Michail, Georgakopoulos-Soares, Ilias, Vasquez, Karen M
Format: Journal Article
Sprache:Englisch
Veröffentlicht: England Oxford University Press 01.05.2025
Oxford Publishing Limited (England)
Schlagworte:
Accessibility
Algorithms
Base Sequence
Biological activity
Computer applications
Deoxyribonucleic acid
DNA
DNA biosynthesis
DNA repair
DNA structure
DNA, Z-Form - chemistry
DNA, Z-Form - genetics
Gene sequencing
Genomic instability
Genomics - methods
Handedness
Humans
Nucleotide sequence
Problem Solving Protocol
Purines
Pyrimidines
Sequence Analysis, DNA - methods
Software
Z-form
web interface
search tool
Z-DNA
algorithm design
ISSN:1467-5463, 1477-4054, 1477-4054
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
Beschreibung
Zusammenfassung:Abstract Z-deoxyribonucleic acid (Z-DNA) is an alternative left-handed DNA structure with a zigzag-shaped backbone that differs from the right-handed canonical B-DNA helix. Z-DNA has been implicated in various biological processes, including transcription, replication, and DNA repair, and can induce genetic instability. Repetitive sequences of alternating purines and pyrimidines have the potential to adopt Z-DNA structures. ZSeeker is a novel computational tool developed for the accurate detection of potential Z-DNA-forming sequences in genomes, addressing key limitations of prior methods, such as computational inefficiency, difficult interpretability and usability, and lack of experimentally generated data. By introducing a novel methodology informed and validated by experimental data, ZSeeker enables the refined detection of potential Z-DNA-forming sequences. Built both as a standalone Python package and as an accessible web interface, ZSeeker allows users to input genomic sequences, adjust detection parameters, and view potential Z-DNA sequence distributions and Z-scores via downloadable visualizations. Our web platform provides a no-code solution for Z-DNA identification, with a focus on accessibility, user-friendliness, speed, and customizability. By providing efficient, high-throughput analysis, and enhanced detection accuracy, ZSeeker has the potential to support significant advancements in understanding the roles of Z-DNA in normal cellular functions, genetic instability, and its implications in human diseases.
Bibliographie:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 14
content type line 23
Guliang Wang and Ioannis Mouratidis are Co-first authors.
ISSN:1467-5463
1477-4054
1477-4054
DOI:10.1093/bib/bbaf240