Danny Incarnato1, Francesco Neri2, Francesca Anselmi1, Salvatore Oliviero1. 1. Human Genetics Foundation (HuGeF), 10126 Torino, Italy and Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, 10123 Torino, Italy. 2. Human Genetics Foundation (HuGeF), 10126 Torino, Italy and.
Abstract
SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: 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 SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: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 SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Yang Wu; Rihao Qu; Yiming Huang; Binbin Shi; Mengrong Liu; Yang Li; Zhi John Lu Journal: Nucleic Acids Res Date: 2016-05-02 Impact factor: 16.971