Resources

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

NEW: RNAcentral (resource), Conserved RNA Structures in Drosophila (resource), RNAbound (resource), Cytoscape stringApp (resource), and WebCircRNA (resource).

Webservers

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

 

Software only

RNAbound


Software

Multiple sequence alignments enhance boundary definition of RNA structures

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

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

 

Databases / data resources

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

Structured RNAs 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

Before 2010


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 RK 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

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

Older servers

distanceP


Webserver

Prediction of distance constraints in proteins

Toy servers

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.

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)