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Related Experiment Video

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RNA Secondary Structure Prediction Using High-throughput SHAPE
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BEAGLE 2.0: A Web Server for RNA Secondary Structure Similarity Detection Leveraging SHAPE-directed RNA Structure

F Ballesio1, A Teofani1, C Carrino1

  • 1Department of Biology, University of Rome "Tor Vergata", Rome, Italy.

Journal of Molecular Biology
|April 23, 2025
PubMed
Summary
This summary is machine-generated.

BEAGLE 2.0 is a web server that aligns RNA secondary structures, enabling searches for structural similarities across diverse biological datasets. This tool aids in discovering RNA homologies and understanding their roles in biological processes.

Keywords:
RNA homology detectionRNA secondary structure alignmentRNA structural similarity searchicSHAPE data integrationnon-coding RNAs (ncRNAs)

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • RNA secondary structures play critical roles in biological and pathological processes.
  • Structural conservation is key for identifying homologies missed by sequence analysis alone.
  • Accurate prediction and comparison of RNA secondary structures are essential.

Purpose of the Study:

  • Introduce BEAGLE 2.0, an enhanced web server for searching RNA secondary structure similarities.
  • Facilitate comparisons between user-provided RNA molecules and extensive biological datasets.
  • Leverage experimentally supported data to identify structural similarities in RNAs.

Main Methods:

  • Utilize the BEAGLE algorithm with BEAR encoding for pairwise RNA secondary structure alignment via dynamic programming.
  • Incorporate diverse datasets including SHAPE-derived structures (human, mouse, zebrafish, bacteria, viruses like SARS-CoV-2), NONCODE predictions, and Rfam-based structures.
  • Accept user input as RNA sequences or secondary structures (dot-bracket or BEAR format).

Main Results:

  • BEAGLE 2.0 provides pairwise alignments with structural similarity measures and statistical significance.
  • Offers visual representations of RNA secondary structures with color-coded elements.
  • Enables efficient searching within large, curated RNA structure datasets.

Conclusions:

  • BEAGLE 2.0 significantly expands the capabilities for RNA secondary structure comparison.
  • Facilitates the discovery of functional RNA similarities using diverse, experimentally validated datasets.
  • Provides a valuable resource for researchers investigating RNA function and evolution.