RNA structurome data analysis bioinformatics software tools
RNA folds into intricate structures that enable its pivotal roles in biology, ranging from regulation of gene expression to ligand sensing and enzymatic functions. Therefore, elucidating RNA structure can provide profound insights into living systems. A recent marriage between…
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ShapeMapper/Sup…
Desktop

ShapeMapper/SuperFold

ShapeMapper converts raw sequencing files into mutational profiles, creates…

ShapeMapper converts raw sequencing files into mutational profiles, creates SHAPE reactivity plots, and provides extensive diagnostic information useful for experiment analysis and troubleshooting.…

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RNAex
Web
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FoldAtlas
Dataset

FoldAtlas

Provides convenient access to in vivo RNA structure probing data across…

Provides convenient access to in vivo RNA structure probing data across thousands of transcripts. FoldAtlas allows a researcher to easily locate, view, and retrieve probing data for a given RNA…

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RNA Framework
Desktop

RNA Framework

Deals with RNA structure probing and post-transcriptional modifications mapping…

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…

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MIMEAnTo
Desktop

MIMEAnTo Mutational Interference Mapping Experiment Analysis Tool

Allows the identification of domains and structures in RNA sequences. MIMEAnTo…

Allows the identification of domains and structures in RNA sequences. MIMEAnTo evaluates MIME data, following error-correction, statistical ascertainment and quality assessment. MIMEAnTo has a…

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SEQualyzer
Desktop

SEQualyzer Structure-profiling Experiment Quality analyzer

A visual and interactive application that makes it easy and efficient to gauge…

A visual and interactive application that makes it easy and efficient to gauge data quality, screen for transcripts with high-quality information and identify discordant replicates in structure…

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RME
Desktop

RME

A tool for RNA secondary structure prediction with multiple types of…

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…

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ProbFold
Desktop

ProbFold

A probabilistic method for RNA secondary structure prediction that integrates…

A probabilistic method for RNA secondary structure prediction that integrates experimental structure probing data. It can be automatically trained given a set of known structures with probing data.…

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StructureFold
Web

StructureFold

Provides an integrated computational solution designed specifically for…

Provides an integrated computational solution designed specifically for large-scale RNA structure mapping and reconstruction across any transcriptome. StructureFold automates the processing and…

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SAVoR
Web

SAVoR Sequencing Annotation and Visualization of RNA structures

An easy-to-use web application that allows the user to visualize RNA-seq data…

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…

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Mod-seeker
Desktop

Mod-seeker

A data analysis pipeline for assaying the structure of RNAs by high-throughput…

A data analysis pipeline for assaying the structure of RNAs by high-throughput sequencing. This technique can be utilized both in vivo and in vitro, with any small molecule that modifies RNA and…

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Spats
Desktop

Spats

Processes reads and calculates SHAPE reactivities for SHAPE-Seq experiments on…

Processes reads and calculates SHAPE reactivities for SHAPE-Seq experiments on multiple RNAs. The Spats package implements a read mapping and reactivity analysis pipeline for calculating SHAPE-Seq…

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ProbeAlign
Desktop

ProbeAlign

An approach to incorporate the reactivities from high-throughput RNA structure…

An approach to incorporate the reactivities from high-throughput RNA structure probing into ncRNA homology search for functional annotation. By incorporating high-throughput sequencing-based…

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RING-MaP
Desktop

RING-MaP RNA interaction groups by mutational profiling

Makes possible single-molecule RNA structure analysis by detecting multiple…

Makes possible single-molecule RNA structure analysis by detecting multiple sites of chemical modification in single RNA strands using massively parallel sequencing. RING-MaP single-molecule nucleic…

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RSF
Desktop

RSF RNA Structure Framework

A modular toolkit developed to deal with RNA structure probing high-throughput…

A modular toolkit developed to deal with RNA structure probing high-throughput data, from reads mapping to structure deconvolution. The RNA Structure Framework main features are 1) automatic…

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SeqFold
Desktop

SeqFold

Predicts RNA secondary structure incorporating current high-throughput RNA…

Predicts RNA secondary structure incorporating current high-throughput RNA structure profiling data, such as PARS, FragSeq, SHAPE-Seq, and conventional SHAPE data. SeqFold was applied to predict RNA…

Curators for RNA structurome analysis

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