RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data.
CONCLUSIONS
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.


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


BACKGROUND
salvatore.oliviero@hugef-torino.org


BACKGROUND
Supplementary data are available at Bioinformatics online.
Human Genetics Foundation (HuGeF), 10126 Torino, Italy and Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, 10123 Torino, Italy.
Danny
D
Incarnato
Human Genetics Foundation (HuGeF), 10126 Torino, Italy and.
Francesco
F
Neri
Human Genetics Foundation (HuGeF), 10126 Torino, Italy and Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, 10123 Torino, Italy.
Francesca
F
Anselmi
Human Genetics Foundation (HuGeF), 10126 Torino, Italy and Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, 10123 Torino, Italy.
Salvatore
S
Oliviero
D019295:Computational Biology / Q000379:methods*; D015894:Genome, Human; D006801:Humans; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome / Q000235:genetics*
D012313:RNA