RNA structurome data analysis software tools

Detects structured noncoding RNAs in comparative genomics data. RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. It can be used in genome wide screens to detect functional RNA structures, as found in noncoding RNAs (ncRNAs) and cis-acting regulatory elements of messenger RNAs (mRNAs). The algorithm allows to calculate thermodynamic stability scores based on a dinucleotide background model.

Deals with RNA structure probing and post-transcriptional modifications mapping high-throughput data. RNA Framework is a modular toolkit. Its main features are (i) automatic reference transcriptome creation, (ii) automatic reads preprocessing (adapter clipping and trimming) and mapping, (iii) scoring and data normalization and (iv) accurate RNA folding prediction by incorporating structural probing data. It can perform not only RNA Structure analysis, but also analysis of RNA post-transcriptional modifications mapping experiments (such as m1A-seq, m6A-seq, 2OMe-seq, and Pseudo-seq).

Enables non-specialists to easily predict RNA secondary structures using cutting-edge high-throughput structure-probing data. Users can easily access and incorporate these data into the RNAex server to enhance the RNA secondary structure prediction using four different folding methods (MaxExpect, SeqFold, RNAstructure (Fold) and RNAfold). RNAex results allow users to clearly view, identify and understand SNP and post-transcriptional regulation sites on the RNA structures. Overall, the server is an early web-based platform for the emerging new field of high-throughput RNA structure-probing analysis.

A tool for RNA secondary structure prediction with multiple types of experimental probing data. RME can use experimental pairing probabilities to restrain the partition function, and predict the structure with maximum restrained expected accuracy based on a MEA algorithm, MaxExpect. It also provides preprocessing scripts for transforming the SHAPE, PARS and DMS-seq data into pairing probability according a posterior probabilistic model. Moreover, it also contains a utility for optimizing the parameters of RME by RME-Optimize.

An easy-to-use web application that allows the user to visualize RNA-seq data and other genomic annotations on RNA secondary structures. SAVoR is designed to help researchers visualize sequencing data in the context of RNA secondary structures.