RNA Structure Framework – automatic transcriptome-scale reconstruction of RNA structures from probing data

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.

Researchers from the Human Genetics Foundation Torino have developed 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.

Overview of the RSF pipeline


Availability – RSF is written in Perl and is freely available under the GPLv3 license from http://rsf.hugef-research.org.

Contact: salvatore.oliviero@hugef-torino.org

Incarnato D, Neri F, Anselmi F, Oliviero S. (2016) RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data. Bioinformatics 32(3):459-61. [abstract]

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