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

Nucleic Acids Res. 2018 Sep 19;46(16):e97. doi: 10.1093/nar/gky486.

Abstract

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. Here we 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, we 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 is available for download at: http://www.rnaframework.com.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Computational Biology / methods*
  • High-Throughput Nucleotide Sequencing / methods*
  • Internet
  • Nucleic Acid Conformation*
  • RNA / chemistry*
  • RNA / genetics
  • RNA / metabolism
  • RNA Processing, Post-Transcriptional*
  • Reproducibility of Results
  • Sequence Analysis, RNA / methods*
  • Software

Substances

  • RNA