RNA Framework – an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications.

RNA is emerging as a key regulator of a plethora of biological processes. While its study has remained elusive for decades, the recent advent of high-throughput sequencing technologies provided the unique opportunity to develop novel techniques for the study of RNA structure and post-transcriptional modifications. Nonetheless, most of the required downstream bioinformatics analyses steps are not easily reproducible, thus making the application of these techniques a prerogative of few laboratories.

Researchers at the Italian Institute for Genomic Medicine introduce RNA Framework, an all-in-one toolkit for the analysis of most NGS-based RNA structure probing and post-transcriptional modification mapping experiments. To prove the extreme versatility of RNA Framework, they applied it to both an in-house generated DMS-MaPseq dataset, and to a series of literature available experiments. Notably, when starting from publicly available datasets, our software easily allows replicating authors’ findings. Collectively, RNA Framework provides the most complete and versatile toolkit to date for a rapid and streamlined analysis of the RNA epistructurome.

RNA Framework features

(A) Ambiguously mapped deletions removal by RNA Framework’s rf-count for the accurate analysis of mutational profiling (MaP) experiments. (B) Schematics of the rf-fold windowed RNA folding approach. (C) Runtimes comparison for ShapeKnots and RNA Framework pseudoknots detection algorithms on a set of 21 randomly generated RNA sequences (3 × 50–100–250–500–750–1000–2000 nucleotides). (D) Sample of the expanded dot-bracket alphabet implemented by RNA Framework to deal with complex topology pseudoknotted RNAs.

Availability – RNA Framework is available for download at: http://www.rnaframework.com.