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Related Experiment Video

Updated: Jul 3, 2025

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

RNA threading with secondary structure and sequence profile.

Zongyang Du¹, Zhenling Peng², Jianyi Yang²

¹Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China.

Bioinformatics (Oxford, England)

|February 11, 2024

Summary

This summary is machine-generated.

RNAthreader is a novel algorithm for RNA threading that improves alignment accuracy and speed. This method enhances RNA 3D structure modeling by efficiently detecting remote homologies.

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RNA Secondary Structure Prediction Using High-throughput SHAPE

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Area of Science:

Computational biology
Bioinformatics
Structural biology

Background:

RNA threading identifies remote homologies for RNA 3D structure modeling.
Current RNA alignment methods are slow, memory-intensive, and lack accuracy, hindering large-scale applications.

Purpose of the Study:

To develop a novel, efficient, and accurate RNA threading algorithm for improved RNA 3D structure modeling.
To address the limitations of existing RNA alignment methods.

Main Methods:

Developed RNAthreader, a novel RNA threading algorithm utilizing RNA secondary structure and sequence profiles.
Introduced a method to simplify RNA secondary structures into compact diagrams for enhanced alignment and reduced memory usage.
Employed a two-step methodology combining integer and dynamic programming for initial and final RNA alignments.

Main Results:

RNAthreader demonstrated superior alignment accuracy compared to existing methods, particularly for RNAs with pseudoknots.
Models built using RNAthreader templates showed lower average RMSD in RNA-Puzzles benchmarks.
RNAthreader achieved significant speed improvements, completing alignments for ~5000 RNAs in under two hours, 3-40 times faster than alternatives.

Conclusions:

RNAthreader is a promising algorithm for efficient and accurate RNA template detection.
The algorithm offers a substantial advancement for large-scale RNA 3D structure modeling and homology detection.