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Updated: Nov 9, 2025
Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms
Published on: February 2, 2024
RNA Framework for Assaying the Structure of RNAs by High-Throughput Sequencing
Tycho Marinus1, Danny Incarnato2
1Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands.
Abstract:
RNA structure is a key player in regulating a plethora of biological processes. A large part of the functions carried out by RNA is mediated by its structure. To this end, in the last decade big effort has been put in the development of new RNA probing methods based on Next-Generation Sequencing (NGS), aimed at the rapid transcriptome-scale interrogation of RNA structures. In this chapter we describe RNA Framework, the to date most comprehensive toolkit for the analysis of NGS-based RNA structure probing experiments. By using two published datasets, we here illustrate how to use the different components of the RNA Framework and how to choose the analysis parameters according to the experimental setup.
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