Resources

This page contains an overview of webservers, software and databases in relation to publications.

Current publications

Webservers

CRISPRon

Webserver and Software

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

WebCircRNA

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

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

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

Software only

CRISPRroots

Post editing on and off-target assessment with RNAseq data

Cytoscape stringApp

Network analysis and visualization of proteomics data

DisLncRF

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

RNAbound

Multiple sequence alignments enhance boundary definition of RNA structures

DotCoder

Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots

RNAscClust

RNAscClust clusters RNAs taking structure conservation into account

RIsearch2

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

RPAsuite

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

Meta RNA Modules

RNA 3D modules in structural alignments

deepBlockAlign

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

RIsearch

RIsearch: Fast search for RNA-RNA interactions

Clasp

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

Databases / data resources

cyanobacteria CRISPRi

This browsers show the CRISPRi-dCas9 results for a genome-wide knockdown experimental series in Synechocystis sp. PCC 6803 under 4% and 30% CO₂ concentrations

Bacillus subtilis PrsA RNAseq data

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

BSGatlas

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

RNAcentral

A hub of information for non-coding RNA sequences

Conserved RNA Structures in Drosophila

Conserved RNA structures in insect genomes

mirnasponge

Predicting clusters of miRNA targets

TISSUES 2.0

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

RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure

miRPD

Software and Data Resource

miRNA-Disease associations inferred from Protein-dicease associations

Structured RNAs in the pig genome

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

TFMirLoop

Predicted miRNA and transcription factor loops

Alternative splicing in the pig

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

Non-coding RNA tracks

Collection of ncRNA predictions in UCSC style

Before 2010

WAR

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

Prediction of distance constraints in proteins

RNA Structure Logos

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

Protein Logos

Visualize the information content of protein sequence alignments

KVL Assembly demo

Sequence assembly for toy purposes

FOLDALIGNM

Multiple global structural alignment of RNA sequences

SARSE

Semi-Automated RNA Sequence Editor

RNA genes

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

Sequence assembly

Supplementary material for the paper Sequence assembly

Micro RNA structurally clustered

MicroRNAs clustered by their structure

cmf_encode

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

PigEST

Porcine EST assembly, expression and SNP data.

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

HM ncRNA scan

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

Piggenome DK

Genomic sequences from the Sino-Danish pig genome project

tmRDB

tmRNP Database local mirror. Includes structural alignment of tmRNA sequences

SRPDB

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

telomDB

Telomerase Database local mirror