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…
Desktop app
G T A T C G C T A Mutational… Mutational Interference Mapping Experiment…

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…

Desktop app
G T A T C G C T A Structure-profiling… Structure-profiling Experiment Quality analyzer

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…

G T A T C G C T A FoldAtlas FoldAtlas

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…

Web app
G T A T C G C T A RNA secondary… RNA secondary structure prediction enhanced by…
Desktop app
G T A T C G C T A ProbFold ProbFold

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.…

Desktop app
G T A T C G C T A RME RME

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…

Desktop app
G T A T C G C T A ProbeAlign ProbeAlign

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…

Desktop app
G T A T C G C T A RNA interaction… RNA interaction groups by mutational profiling

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…

Desktop app
G T A T C G C T A ShapeMapper/SuperFold ShapeMapper/SuperFold

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.…

Desktop app
G T A T C G C T A Mod-seeker Mod-seeker

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…

Web app
G T A T C G C T A Sequencing Annotation… Sequencing Annotation and Visualization of RNA…

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…

Web app
G T A T C G C T A StructureFold StructureFold

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…

Desktop app
G T A T C G C T A RNA Structure… RNA Structure Framework

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…

Desktop app
G T A T C G C T A SeqFold Deprecated SeqFold

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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