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Software

HSA

A flexible tool that can jointly analyze multiple contact maps from Hi-C experiments to infer the 3D chromatin structure of the genome. [web]

Reference: Zou C, Zhang Y, Ouyang Z (2016) HSA: integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure. Genome Biology, 17:40  [ web]

SeqFold

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. [web]

Reference: Ouyang Z, Snyder MP, and Chang HY (2013) SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data.Genome Research, 23:377-387. Published in Advance October 11, 2012.  [ web]