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RNA-RNA interaction prediction software tools | Structure data analysis

Considerable attention has been focused on predicting RNA-RNA interaction since it is a key to identifying possible targets of non-coding small RNAs that regulate gene expression post-transcriptionally. A number of computational studies have so far…
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PETcofold
Web
Desktop

PETcofold

Predicts the joint secondary structure including RNA-RNA interactions.…

Predicts the joint secondary structure including RNA-RNA interactions. PETcofold is a computational method which identifies evolutionary conserved structures and can exploit the information from…

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NPInter
Dataset

NPInter Noncoding RNAs and Protein related biomacromolecules Interaction

Catalogs experimentally determined functional interactions between ncRNAs and…

Catalogs experimentally determined functional interactions between ncRNAs and proteins, mRNAs or genomic DNA sequences. NPInter integrates the diverse body of experimental knowledge about functional…

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IntaRNA
Web

IntaRNA

A program for the fast and accurate prediction of interactions between two RNA…

A program for the fast and accurate prediction of interactions between two RNA molecules. It has been designed to predict mRNA target sites for given non-coding RNAs (ncRNAs) like eukaryotic…

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RNAhybrid
Web

RNAhybrid

A tool for finding the minimum free energy hybridization of a long and a short…

A tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, ie. the short sequence is hybridized to the best fitting…

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RactIPAce
Desktop

RactIPAce RNA– RNA interACTions Integer Programming AcCEssibility

A based prediction model of RNA-RNA interactions. RactIPAce achieves the best…

A based prediction model of RNA-RNA interactions. RactIPAce achieves the best predictive performance on the newly compiled dataset of experimentally verified interactions in the literature as…

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RISE
Dataset

RISE RNA Interactome from Sequencing Experiments

Provides RNA-RNA interactions (RRIs) identified through high-throughput…

Provides RNA-RNA interactions (RRIs) identified through high-throughput sequencing technologies. RISE is a comprehensive database of RNA interactome from sequencing experiments. It includes (i)…

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LRIscan
Desktop

LRIscan Long-range RNA-RNA interactions scan

A tool for the Long-range RNA-RNA interactions (LRI) prediction in full viral…

A tool for the Long-range RNA-RNA interactions (LRI) prediction in full viral genomes based on a multiple genome alignment. LRIscan offers the opportunity to predict possible LRIs under certain…

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RAID
Dataset

RAID RNA Association Interaction Database

Provides RNA-associated (RNA-RNA/RNA-protein) interaction database. RAID…

Provides RNA-associated (RNA-RNA/RNA-protein) interaction database. RAID intends to provide the scientific community with all-in-one resources for efficient browsing and extraction of the…

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ViennaRNA
Desktop
Web

ViennaRNA

A widely used collection of programs for thermodynamic RNA secondary structure…

A widely used collection of programs for thermodynamic RNA secondary structure prediction. Over the years, many additional tools have been developed building on the core programs of the package to…

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CopraRNA
Web

CopraRNA Comparative prediction algorithm for small RNA targets

A tool for sRNA target prediction. It computes whole genome predictions by…

A tool for sRNA target prediction. It computes whole genome predictions by combination of distinct whole genome IntaRNA predictions. As input, CopraRNA requires at least 3 homologous sRNA sequences…

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RIblast
Desktop

RIblast

A package to predict RNA-RNA interaction. RIblast is based on…

A package to predict RNA-RNA interaction. RIblast is based on seed-and-extension algorithm for comprehensive lncRNA interactome analysis. It consists of database construction search step and RNA…

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EPLMI
Desktop

EPLMI

Predicts new lncRNA-miRNA interactions and computes the putative interaction…

Predicts new lncRNA-miRNA interactions and computes the putative interaction strength of known lncRNA-miRNA interactions. EPLMI is based on known lncRNA-miRNA interaction network. It can be useful…

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RNA workbench
Server

RNA workbench

Establishes a central, redistributable workbench for scientists and programmers…

Establishes a central, redistributable workbench for scientists and programmers working with RNA-related data. The RNA workbench builds a sustainable community around it. This platform is unique in…

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ASSA
Desktop

ASSA Antisense Search Approach

Concerns the thermodynamics-based prediction of the RNA-RNA interactions on a…

Concerns the thermodynamics-based prediction of the RNA-RNA interactions on a transcriptome scale. The general idea of Antisense Search Approach (ASSA) is to first identify putative antisense sites…

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RNAplex
Desktop

RNAplex

A tool especially created to rapidly search for short interactions between two…

A tool especially created to rapidly search for short interactions between two long RNAs. RNAplex uses a slightly different energy model which reduces the computational time by a factor 10-27…

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PLEXY
Desktop

PLEXY

Computes thermodynamically optimal interactions of a box C/D snoRNA with a…

Computes thermodynamically optimal interactions of a box C/D snoRNA with a putative target RNA. PLEXY extracts the putative antisense elements (ASEs) from a snoRNA sequence with annotated box-motifs…

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PairFold
Web

PairFold

Predicts the secondary structure of a pair of RNA or DNA molecules. Extending…

Predicts the secondary structure of a pair of RNA or DNA molecules. Extending the notion of secondary structure for a single molecule, a secondary structure for a pair of molecules (R1, R2) is a set…

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IRBIS
Desktop

IRBIS Intermolecular RNA (BLAT-like) Interaction Search

A computational pipeline for detecting conserved complementary regions in…

A computational pipeline for detecting conserved complementary regions in unaligned orthologous sequences. Unlike other methods, IRBIS follows the "first-fold-then-align" principle in which…

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GUUGle
Desktop
Web

GUUGle

Locates potential helical regions under RNA base pairing rules, which include…

Locates potential helical regions under RNA base pairing rules, which include Watson-Crick as well as G-U pairs. GUUGle accepts a positive and a negative set of sequences, and determines all exact…

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RIsearch
Desktop

RIsearch

Searches fast RNA-RNA interaction. RIsearch employs a modified…

Searches fast RNA-RNA interaction. RIsearch employs a modified Smith-Waterman-Gotoh algorithm based on di-nucleotides to approximate nearest-neighbor energy parameters. The software focuses on…

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RILogo
Desktop
Web

RILogo

A program to visualize inter- and intramolecular base pairing between two RNA…

A program to visualize inter- and intramolecular base pairing between two RNA molecules. The input for RILogo is a pair of structure-annotated sequences or alignments. In the latter case, RILogo…

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RNAup
Desktop

RNAup

Calculates the thermodynamics of RNA−RNA interactions, by decomposing the…

Calculates the thermodynamics of RNA−RNA interactions, by decomposing the binding into two stages. First the probability that a potential binding sites remains unpaired (equivalent to the free…

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RactIP
Desktop
Web

RactIP

A fast and accurate prediction method for RNA-RNA interaction of general type…

A fast and accurate prediction method for RNA-RNA interaction of general type using integer programming. RactIP can integrate approximate information on an ensemble of equilibrium joint structures…

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RNA…
Web

RNA Interaction Network Fidelity

Calculates the interaction network fidelity (INF) between two RNA 3-D…

Calculates the interaction network fidelity (INF) between two RNA 3-D structures based on their annotations. RNA Interaction Network Fidelity is a method available via a web interface.

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bistaRNA
Desktop

bistaRNA

A method for predicting multiple binding sites of target RNAs. bistaRNA employs…

A method for predicting multiple binding sites of target RNAs. bistaRNA employs binding profiles that represent scores for hybridized structures, leading to reducing the computational cost for…

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RNAcofold
Web

RNAcofold

Predicts secondary structures of single stranded RNA or DNA sequences upon…

Predicts secondary structures of single stranded RNA or DNA sequences upon dimer formation. In contrast to earlier approaches, complex internal structures in both RNAs are fully taken into account.…

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RRDB
Dataset

RRDB RNA-RNA Docking Benchmark

RRDB is comprehensive and nonredundant RNA-RNA docking benchmark. This dataset…

RRDB is comprehensive and nonredundant RNA-RNA docking benchmark. This dataset was organized into three different groups according to the interface conformational changes between bound and unbound…

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