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- Title
RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data.
- Authors
Incarnato, Danny; Neri, Francesco; Anselmi, Francesca; Oliviero, Salvatore
- 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.
- Subjects
MOLECULAR structure of RNA; GENETIC transcription; GENE expression; DATA analysis; RNA sequencing
- Publication
Bioinformatics, 2016, Vol 32, Issue 3, p459
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btv571