Introduction

The rapidly increasing number of discovered non-coding RNAs makes the understanding of their structure a key feature toward a deeper comprehension of gene expression regulation. Various enzymatic- and chemically- based approaches have been recently developed to allow whole-genome studies of RNA secondary structures. Several methods have been recently presented that allow high-throughput RNA structure probing (CIRS-seq, Structure-seq, SHAPE-seq, PARS, etc.) and unbiased structural inference of residues within RNAs in their native conformation. We here present an analysis toolkit, named RNA Structure Framework (RSF), which allows fast and fully-automated analysis of high-throughput structure probing data, from data pre-processing to whole-transcriptome RNA structure inference.RSF is written in Perl and is freely available under the GPLv3 license from http://rsf.hugef-research.org.salvatore.oliviero@hugef-torino.orgSupplementary data are available at Bioinformatics online.

Publications

  1. RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data.
    Cite this
    Incarnato D, Neri F, Anselmi F, Oliviero S, 2016-02-01 - Bioinformatics (Oxford, England)

Credits

  1. Danny Incarnato
    Developer

    Human Genetics Foundation (HuGeF), 10126 Torino, Italy

  2. Francesco Neri
    Developer

    Human Genetics Foundation (HuGeF), 10126 Torino, Italy

  3. Francesca Anselmi
    Developer

    Human Genetics Foundation (HuGeF), 10126 Torino, Italy

  4. Salvatore Oliviero
    Investigator

    Human Genetics Foundation (HuGeF), 10126 Torino, Italy

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Summary
AccessionBT000847
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Country/RegionItaly
Submitted BySalvatore Oliviero