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RNA Secondary Structure Prediction Using High-throughput SHAPE
Published on: May 31, 2013
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A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs
Riccardo Delli Ponti1,2, Alexandros Armaos1,2, Stefanie Marti1,2
1Centre for Genomic Regulation, Bioinformatics and Genomics Programme, The Barcelona Institute for Science and Technology, Barcelona, Spain.
Frontiers in Molecular Biosciences
|December 19, 2018
Summary
CROSSalign is a new method for comparing RNA secondary structures. It accurately identifies similarities between RNA molecules of varying lengths, outperforming existing methods.
Area of Science:
- Computational Biology
- Bioinformatics
- Molecular Biology
Background:
- RNA secondary structure plays a crucial role in molecular function.
- Comparing RNA structures is essential for understanding evolutionary relationships and functional conservation.
- Existing methods face challenges in accurately aligning and comparing RNA secondary structure profiles, especially for molecules of different lengths.
Purpose of the Study:
- To develop and present a novel computational method, CROSSalign, for comparing RNA secondary structure profiles.
- To assess the efficacy of CROSSalign in identifying structural similarities and homologs across diverse RNA molecules.
- To investigate the structural conservation of specific long non-coding RNAs and ssRNA viruses using the CROSSalign method.
Main Methods:
- The CROSSalign method combines the Computational Recognition Of Secondary Structure (CROSS) algorithm for predicting RNA secondary structure profiles at single-nucleotide resolution.
- Dynamic Time Warping (DTW) is employed to align RNA secondary structure profiles of varying lengths.
- Pair-wise comparisons are performed to identify homologous regions and similarities between RNA sequences.
Main Results:
- CROSSalign accurately identifies conserved regions, such as repeat A of XIST and domain D2 of HOTAIR, within RNA sequences.
- The method demonstrates superior performance compared to covariance modeling-based approaches for detecting structural similarities.
- CROSSalign successfully identifies homologs and regions of similarity between RNA profiles of different lengths, even among thousands of comparisons.
Conclusions:
- CROSSalign provides a robust and accurate approach for comparing RNA secondary structure profiles.
- The method enhances the ability to investigate structural conservation in ncRNAs and viral RNAs.
- CROSSalign offers a valuable tool for RNA bioinformatics research, with the algorithm freely available.
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