SeqFold: Genome-scale reconstruction of RNA secondary structure integrating experimental measurements

SeqFold is a tool for RNA secondary structure prediction from experimental data. Given high-throughput data, it can reconstruct the secondary structures of the whole transcriptome, termed the RNA structurome. It outputs reconstructed RNA secondary structure as well as base-level accessibilities for each transcript. Input data types include parallel analysis of RNA structure (PARS), selective 2’-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq), fragmentation sequencing (FragSeq), and conventional SHAPE data.