General Information
| Description | Automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data |
| Homepage | http://rsf.hugef-research.org |
Publications
RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data
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.
Related Tools
StatAlign 2.0
Published January 2013
Combining statistical alignment with RNA secondary structure prediction
StructureFold
Published April 2015
Genome-wide RNA secondary structure mapping and reconstruction in vivo
ProbFold
Published April 2016
A probabilistic method for integration of probing data in RNA secondary structure prediction
FAIR Evaluation
Sorry, you must be signed in to evaluate this object.
