Structural bioinformatics StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo

Motivation: RNAs fold into complex structures that are integral to the diverse mechanisms under-lying RNA regulation of gene expression. Recent development of transcriptome-wide RNA struc-ture profiling through the application of structure-probing enzymes or chemicals combined with high-throughput sequencing has opened a new field that greatly expands the amount of in vitro and in vivo RNA structural information available. The resultant datasets provide the opportunity to investigate RNA structural information on a global scale. However, the analysis of high-throughput RNA structure profiling data requires considerable computational effort and expertise. Results:We present a new platform, StructureFold, that provides an integrated computational solu-tion designed specifically for large-scale RNA structure mapping and reconstruction across any transcriptome. StructureFold automates the processing and analysis of raw high-throughput RNA structure profiling data, allowing the seamless incorporation of wet-bench structural information from chemical probes and/or ribonucleases to restrain RNA secondary structure prediction via the RNAstructure and ViennaRNA package algorithms. StructureFold performs reads mapping and alignment, normalization and reactivity derivation, and RNA structure prediction in a single user