SEISMICgraph: a web-based tool for RNA structure data visualization

Data consists of a DMS-MaPseq experiment of a library of 29 predicted riboswitches that were predicted to bind to Mg2+, 30 more proposed to respond to purines, and 22 other well-known structures such as the add riboswitch from Vibrio vulnificus or the HIV FSE. The library was in vitro transcribed using regular uridine, pseudouridine, or N1-methylpseudouridine. RNAs were then denatured at 95C, refolded in the presence or absence of adenine, and DMS treated. Reverse transcription was done using Induro RT (NEB), which introduces mutations at the DMS modified bases. The samples were then indexed using NEBNext Ultra II DNA Library Prep Kit and sequenced in an Illumina NextSeq 1000. Sequencing data was analyzed using SEISMIC-RNA and SEISMICgraph.