3plex Web: An Interactive Platform for RNA:DNA Triplex Prediction and Analysis
Journal:
arXiv
Published Date:
Apr 25, 2025
Abstract
Summary: Long non-coding RNAs (lncRNAs) exert their functions by cooperating
with other molecules including proteins and DNA. Triplexes, formed through the
interaction between a single-stranded RNA (ssRNA) and a double-stranded DNA
(dsDNA), have been consistently described as a mechanism that allows lncRNAs to
target specific genomic sequences in vivo. Building on the computational tool
3plex, we developed 3plex Web, an accessible platform that enhances RNA:DNA
triplex prediction by integrating interactive visualization, statistical
evaluation, and user-friendly downstream analysis workflows. 3plex Web
implements new features such as input randomization for statistical
assessments, interactive profile plotting for triplex stability, and
customizable DNA Binding Domain (DBD) selection. This platform enables rapid
analysis through PATO, substantially reducing processing times compared to
previous methods, while offering Snakemake workflows to integrate gene
expression data and explore lncRNA regulatory mechanisms.
Availability and implementation: 3plex Web is freely available at
https://3plex.unito.it as an online web service. The source code for 3plex is
available at https://github.com/molinerisLab/3plex, paired with a definition
file to set up the application into a Singularity image.
Contact: [email protected]
Keywords: DNA; RNA; RNA-DNA interaction; triplex; long non-coding RNA;
lncRNA; gene regulation; web application
