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 in vivo RNA structure probing and next-generation sequencing (NGS) has revolutionized the RNA field by enabling transcriptome-wide structure determination in vivo, which has been applied to date to human cells, yeast cells, and Arabidopsis seedlings. Analysis of resultant in vivo 'RNA structuromes' provides new and important information regarding myriad cellular processes, including control of translation, alternative splicing, alternative polyadenylation, energy-dependent unfolding of mRNA, and effects of proteins on RNA structure.
Source text:
(Kwoket al., 2015) The RNA structurome: transcriptome-wide structure probing with next-generation sequencing. Trends Biochem Sci.
Detects structured noncoding RNAs in comparative genomics data. RNAz is a…
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…
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.…
Enables non-specialists to easily predict RNA secondary structures using…
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…
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…
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…
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…
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…
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…
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…
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.…
Methods for statistically modeling these structure-probing data and extracting…
Methods for statistically modeling these structure-probing data and extracting structural features from them.
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…
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…
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…
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…
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…
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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