Resources

CRISPRon

Webserver and Software

CRISPR-Cas9 gRNA efficiency prediction webserver based on data integration and deep learning

WebCircRNA

Webserver

Assessing the circular RNA potential of coding and noncoding RNA

CRISPRoff

Webserver and Software

CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters

RAIN

Webserver

Searching RNA-protein interactions in STRING integrated framework

Foldalign 2.5

Webserver and Software

Foldalign 2.5: Parallel version of Foldalign for structural alignment of RNA sequences

RNAcop

Webserver and Software

RNAcop: Optimizing RNA structures by sequence extensions

RNAsnp

Webserver and Software

Identifying local RNA structures disrupted by SNPs

DeepBlockAlign for miRNAs

Webserver

Compare RNA-seq data to a database of pre-compiled miRNA RNA-seq profiles

RILogo

Webserver and Software

Visualising RNA-RNA interactions

PETfold

Webserver and Software

Phylogenetic, Evolu­tionary and Ther­mo­dy­na­mic fol­ding of a multiple alignment of RNA se­quen­ces. Improved version 2.0 now available resulting in a significant speed improvement

MaxAlike

Webserver and Software

Phylogenetic reconstruction of in­com­plete sequences by maximum like­li­hood

PETcofold

Webserver and Software

Integrated frame­work with PETfold to fold and search for RNA-RNA interac­tions between two multiple alignments of RNA se­quen­ces

CRISPRroots

Software

Post editing on and off-target assess­ment with RNAseq data

Cytoscape stringApp

Software

Network analysis and visualization of proteomics data

DisLncRF

Software

Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles

RNAbound

Software

Multiple sequence alignments enhance boundary definition of RNA structures

RNAscClust

Software

RNAscClust clusters RNAs taking structure conservation into account

RIsearch2

Software

Large-scale prediction of RNA-RNA interactions and siRNA off-targets

RPAsuite

Software

Differential and coherent processing: Analyzing RNAseq data for pattern differences from different samples

Meta RNA Modules

Software

RNA 3D modules in structural alignments

deepBlockAlign

Software

A tool for aligning RNA-seq profiles of read block patterns

RIsearch

Software

RIsearch: Fast search for RNA-RNA interactions

Clasp

Software

Fast local fragment chaining using sum-of-pair gap costs

Bacillus subtilis PrsA RNAseq data

Data Resource

RNA-seq dataset for a study of the impact of PrsA over-expression on the Bacillus subtilis transcriptome

BSGatlas

Data Resource

A unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access

RNAcentral

Data Resource

A hub of information for non-coding RNA sequences

Conserved RNA Structures in Drosophila

Data Resource

Conserved RNA structures in insect genomes

mirnasponge

Data Resource

Predicting clusters of miRNA targets

TISSUES 2.0

Data Resource

Tissue expression database integrating multiple sources of evidence for human, mouse, rat and pig

Conserved RNA Structures (CRSs) in the vertebrate genome

Data Resource and Supplement

Conserved RNA structures in vertebrate genomes

miRPD

Software and Data Resource

miRNA-Disease associations inferred from Protein-dicease associations

Structured RNAs in the pig genome

Data Resource

Annotation of structured RNAs in the pig genome by sequence, structrure homology, RNAseq data and de novo predictions

TFMirLoop

Data Resource

Predicted miRNA and transcription factor loops

Alternative splicing in the pig

Data Resource

Supplementary data for the paper A study of alternative splicing in the pig

Non-coding RNA tracks

Data Resource

Collection of ncRNA predictions in UCSC style

WAR

Webserver

Webserver for aligning structural RNAs

FOLDALIGN

Webserver and Software

Pairwise local and global structural alignment of RNA sequences.

• FOLDALIGN: Pairwise local and global structural alignment of RNA sequences.
• FOLDALIGNM: Multiple glo­bal struc­tu­ral a­lign­ment of RNA se­quences

The R_K Page

Webserver and Software

Computing the K category correlation coefficient

RNAdbtool

Webserver and Software

Semi-automated update and cleanup of structural RNA databases

MatrixPlot

Webserver and Software

Visualize sequence and structure constraints

distanceP

Webserver

Prediction of distance constraints in proteins

RNA Structure Logos

Webserver

Visualize the information content of DNA and RNA sequence and structure alignment

Protein Logos

Webserver

Visualize the information content of protein sequence alignments

KVL Assembly demo

Webserver

Sequence assembly for toy pur­poses

FOLDALIGNM

Software

Multiple glo­bal struc­tu­ral a­lign­ment of RNA se­quences

SARSE

Software

Semi-Automated RNA Sequence Editor

RNA genes

Data Resource

Supplementary material for the paper The tedious task of finding homologous noncoding RNA genes

Sequence assembly

Data Resource

Supplementary material for the paper Sequence assembly

Micro RNA structurally clustered

Data Resource

MicroRNAs clustered by their structure

cmf_encode

Data Resource

CMfinder predicted conserved RNA structures in the ENCODE regions using RNA structure constraints

PigEST

Data Resource

Porcine EST assembly, expression and SNP data.

• PigESTncRNA: Noncoding RNAs.
• PigESTmap: Genomic mappings.
• PigESTmito: Porcine mitochon­dria. Expression and SNPs.

HM ncRNA scan

Data Resource

Predicted conserved RNA structures in corresponding region between human and mouse unalignable in primary sequence

Piggenome DK

Data Resource

Genomic sequences from the Sino-Danish pig genome project

tmRDB

Database

tmRNP Database local mirror. In­clu­des struc­tural a­lign­ment of tmRNA sequences

SRPDB

Database

Signal recognition particle database local mirror. In­clu­des struc­tural a­lign­ment of the SRP RNA sequences

telomDB

Database

Telomerase Database local mirror