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Secondary structure prediction software tools | RNA data analysis

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MC-Cons
Web

MC-Cons

Identifies cloverleaf structure for each sequence. MC-Cons computes a program…

Identifies cloverleaf structure for each sequence. MC-Cons computes a program that assigns an RNA secondary structure among sub-optimals for many sequences, such that the assigned secondary…

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MC-Sym
Web

MC-Sym Macromolecular Conformations by SYMbolic programming

Generates a set of 3-D structure models from a syntactic definition of the…

Generates a set of 3-D structure models from a syntactic definition of the modeled RNA molecule. MC-Sym is an RNA 3-D structure modeling system. It creates a conformational search space from this…

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MC-Fold
Web

MC-Fold

Predicts RNA secondary structures from sequence. MC-Fold is a part of an…

Predicts RNA secondary structures from sequence. MC-Fold is a part of an RNA-structure-prediction method based on nucleotide cyclic motifs (NCMs). This application is implemented as a pipeline with…

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RNAstructure
Desktop
Web

RNAstructure

Allows RNA secondary structure prediction and analysis. RNAstructure is…

Allows RNA secondary structure prediction and analysis. RNAstructure is designed to make algorithms accessible for a variety of user needs. The software includes methods for predicting bimolecular…

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R-scape
Desktop

R-scape RNA Structural Covariation Above Phylogenetic Expectation

A computational method that quantitatively tests whether covariation analysis…

A computational method that quantitatively tests whether covariation analysis supports the presence of a conserved RNA secondary structure. R-scape analyzes a multiple-RNA sequence alignment and…

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RNAz
Desktop

RNAz

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…

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Centroid RNA…
Desktop

Centroid RNA package

Secondary structure prediction for aligned RNA sequences.

Secondary structure prediction for aligned RNA sequences.

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MC-Fold-DP
Desktop

MC-Fold-DP

A RNA secondary structure prediction tool based on the idea of combining small…

A RNA secondary structure prediction tool based on the idea of combining small motifs, called nucleotide cyclic motifs (NCMs). The algorithm implemented here has polynomial runtime in O(n^3) and uses…

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CROSS
Web

CROSS Computational Recognition of Secondary Structure

Calculates the structural profile of an RNA sequence (single- or…

Calculates the structural profile of an RNA sequence (single- or double-stranded state) at single-nucleotide resolution and without sequence length restrictions. CROSS algorithm is an artificial…

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CentroidFold
Web

CentroidFold

Predicts an RNA secondary structure from an RNA sequence.

Predicts an RNA secondary structure from an RNA sequence.

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PHMMTS
Desktop

PHMMTS Pair Hidden Markov Models on Tree Structures

Allows RNA structural alignment. PHMMTS is an approach based on conditional…

Allows RNA structural alignment. PHMMTS is an approach based on conditional random fields (CRFs). PHMMTS is an algorithm for structural alignment of a binary tree and a sequence, and has been applied…

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CONTRAfold
Desktop
Web

CONTRAfold

A novel secondary structure prediction method based on conditional log-linear…

A novel secondary structure prediction method based on conditional log-linear models (CLLMs).

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Carnac
Desktop

Carnac

A software tool for analysing the hypothetical secondary structure of a family…

A software tool for analysing the hypothetical secondary structure of a family of homologous RNA.

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Dynalign
Desktop

Dynalign

Aligns two sequences and finds a common structure, including multibranch loops.…

Aligns two sequences and finds a common structure, including multibranch loops. Dynalign is a dynamic programming algorithm that uses nearest-neighbor rules for predicting the free energies of…

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RNApdbee
Web

RNApdbee

Allows to extract RNA secondary structure from the pdb file, and presents it in…

Allows to extract RNA secondary structure from the pdb file, and presents it in both textual and graphical form. RNApdbee supports processing of knotted and unknotted structures of large RNAs, also…

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Rtools
Web

Rtools

Performs various secondary structural analyses on single RNA sequences by…

Performs various secondary structural analyses on single RNA sequences by CentroidFold, CentroidHomfold, IPKnot, CapR, Rchange, Raccess and RintD. By just giving an RNA sequence to the web server,…

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PETfold/PETcofo…
Web

PETfold/PETcofold

The Probabilistic Evolutionary and Thermodynamic (PET) model unifies…

The Probabilistic Evolutionary and Thermodynamic (PET) model unifies evolutionary and thermodynamic information about RNA secondary structures in one probabilistic model.

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CentroidHomfold
Desktop
Web

CentroidHomfold

A method which includes information about homologous sequences into the…

A method which includes information about homologous sequences into the prediction of the secondary structure of the target sequence, and showed that it substantially improved the performance of…

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The…
Desktop

The super-n-motifs model

Provides an efficient way of comparing secondary structures from linear and…

Provides an efficient way of comparing secondary structures from linear and circular RNA comprising pseudoknots and G-quadruplex (G4s). The super-n-motifs model is based on the idea that similar…

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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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MaxExpect
Web

MaxExpect

Predicts RNA secondary structure by maximizing the expected base-pair accuracy.

Predicts RNA secondary structure by maximizing the expected base-pair accuracy.

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RNA Sampler
Desktop

RNA Sampler

A sampling based program that predicts common RNA secondary structure motifs in…

A sampling based program that predicts common RNA secondary structure motifs in a group of related sequences.

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RNAfold
Web

RNAfold

Allows prediction of secondary structures of single stranded RNA or DNA…

Allows prediction of secondary structures of single stranded RNA or DNA sequences.

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RNAalifold
Web

RNAalifold

Predicts the structure common to most of the sequences in an alignment.…

Predicts the structure common to most of the sequences in an alignment. RNAalifold combines a thermodynamic energy minimization with a simple scoring model to assess evolutionary conservation. It…

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MASTR
Web

MASTR Multiple Alignment of STructural RNAs

Performs multiple alignment and secondary structure prediction on a set of…

Performs multiple alignment and secondary structure prediction on a set of structural RNA sequences.

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Multilign
Web

Multilign

An algorithm to find the lowest free energy RNA secondary structure common to…

An algorithm to find the lowest free energy RNA secondary structure common to multiple sequences.

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PPfold
Desktop

PPfold

It can predict the consensus secondary structure of RNA alignments through a…

It can predict the consensus secondary structure of RNA alignments through a stochastic context-free grammar coupled to an evolutionary model.

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RNAwolf
Desktop

RNAwolf

A theoretical model capturing both RNA pair families and extended secondary…

A theoretical model capturing both RNA pair families and extended secondary structure motifs with shared nucleotides using 2-diagrams. RNAwolf was compared to three state-of-the-art thermodynamic…

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PSTAG
Web
Desktop

PSTAG Pair Stochastic Tree Adjoining Grammars

Allows alignment and prediction of RNA structures including pseudoknots. PSTAG…

Allows alignment and prediction of RNA structures including pseudoknots. PSTAG extends the software PHMMTSs (pair hidden Markov models on tree structures). The implementation of PSTAG employs a…

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RNASLOpt
Desktop

RNASLOpt

A program for predicting stable local optimal secondary structures for RNAs.

A program for predicting stable local optimal secondary structures for RNAs.

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TurboFold
Web

TurboFold

An iterative probabilistic method for predicting secondary structures for…

An iterative probabilistic method for predicting secondary structures for multiple RNA sequences that efficiently and accurately combines the information from the comparative analysis between…

XRate
Desktop

XRate

Allows users to perform phylogenetic comparative genomics. Xrate is a package…

Allows users to perform phylogenetic comparative genomics. Xrate is a package that permits to provide maximum-likelihood analysis of multiple alignments and phylogenies using phylo-grammars as well…

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Advanced_multil…
Desktop

Advanced_multiloops

Predicts RNA secondary structure. Advanced_multiloops permits to avoid isolated…

Predicts RNA secondary structure. Advanced_multiloops permits to avoid isolated base pairs. It includes the free energy change contributions of coaxial stacking, dangling ends, terminal mismatches,…

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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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RNAView
Desktop

RNAView

Generates 2-dimensional displays of RNA/DNA secondary structures with tertiary…

Generates 2-dimensional displays of RNA/DNA secondary structures with tertiary interactions.

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Pfold
Web

Pfold

Takes an alignment of RNA sequences as input and predicts a common structure…

Takes an alignment of RNA sequences as input and predicts a common structure for all sequences. Pfold is based on the KH-99 algorithm, which was only useful for a limited number of sequences due to…

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Rtips
Desktop
Web

Rtips

A web-based tool for fast and accurate prediction of RNA 2D complex structures.…

A web-based tool for fast and accurate prediction of RNA 2D complex structures. Rtips comprises two computational tools based on integer programming, IPknot for predicting RNA secondary structures…

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RNAlocopt
Web

RNAlocopt

Samples a user-specified number of structures from the Boltzmann subensemble of…

Samples a user-specified number of structures from the Boltzmann subensemble of all locally optimal structures. RNAlocopt is an efficient algorithm to compute the partition function over all…

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RNAprob
Desktop

RNAprob

Predicts data-directed RNA secondary structure. RNAprob uses direct…

Predicts data-directed RNA secondary structure. RNAprob uses direct likelihood-based calculations of pseudo-energy terms per considered structural context. It eliminates the need for parameter…

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PR2S2Clust
Desktop

PR2S2Clust Patched RNA-seq Read Segments' Structure-oriented Clustering

Extracts features to prepare the secondary structure profiles of the RNA-seq…

Extracts features to prepare the secondary structure profiles of the RNA-seq read segments. PR2S2Clust provides a strategy to employ the profiles to annotate the segments into ncRNA classes using…

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RDfolder
Web

RDfolder

Predicts RNA secondary structure. RDfolder is a web server which provides two…

Predicts RNA secondary structure. RDfolder is a web server which provides two methods for prediction of RNA secondary structure: random stacking of helical and helical regions distribution. The…

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vsfold
Web

vsfold

A program to calculate optimal RNA secondary structures. vsfold uses…

A program to calculate optimal RNA secondary structures. vsfold uses di-nucleotide pairing energies as with most traditional approaches. For long-range entropy interactions, the approach uses an…

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Vfold
Web
Desktop

Vfold

Provides a user friendly tool for the prediction of RNA structure and…

Provides a user friendly tool for the prediction of RNA structure and stability. Vfold offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b)…

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RNABP COGEST
Dataset

RNABP COGEST RNA Base Pair Count, Geometry and Stability

Brings together information, extracted from literature data, regarding…

Brings together information, extracted from literature data, regarding occurrence frequency, experimental and quantum chemically optimized geometries, and computed interaction energies, for…

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ILM
Desktop

ILM Iterative Loop Matching

Predicts RNA secondary structures including pseudoknots. ILM can not only…

Predicts RNA secondary structures including pseudoknots. ILM can not only predict consensus structures for aligned homologous sequences, using combined thermodynamic and covariance scores, but can…

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Rfold
Desktop

Rfold

Computes local base pairing probabilities for long DNA sequences. Rfold…

Computes local base pairing probabilities for long DNA sequences. Rfold implements an algorithm that exactly computes the base pairing probabilities associated with the energy model under the…

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RNAG
Desktop
Web

RNAG

A global structural alignment algorithm to predict consensus secondary…

A global structural alignment algorithm to predict consensus secondary structures for unaligned sequences. RNAG uses a blocked Gibbs sampling algorithm, which has a theoretical advantage in…

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KNetFold
Desktop
Web

KNetFold

A software tool for predicting the consensus RNA secondary structure for a…

A software tool for predicting the consensus RNA secondary structure for a given alignment of nucleotide sequences. The input to the network is the mutual information, the fraction of complementary…

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inteRNA
Web

inteRNA

Aims to compute the joint structure prediction of two given RNA sequences…

Aims to compute the joint structure prediction of two given RNA sequences through minimizing their total free energy. inteRNA aims to minimize the joint free energy under a number of energy models…

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RNAforester
Web
Desktop

RNAforester

Compares RNA secondary structures. RNAforester supports the computation of…

Compares RNA secondary structures. RNAforester supports the computation of pairwise and multiple alignment of structures based on the tree alignment model. The user interface follows the philosophy…

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rPredictor
Web

rPredictor

A bioinformatic infrastructure for prediction, analysis and storage of…

A bioinformatic infrastructure for prediction, analysis and storage of secondary structures of ribosomal RNAs. rPredictor includes a ribosomal RNA (rRNA) structure prediction engine based on the…

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COVE
Desktop

COVE

Uses as an implementation of stochastic context free grammar methods for RNA…

Uses as an implementation of stochastic context free grammar methods for RNA sequence/structure analysis. COVE is an extremely sensitive tool for database searching for homologous RNAs. It requires…

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RNAEAPath
Desktop

RNAEAPath

Predicts low energy barrier folding pathways between conformational structures.…

Predicts low energy barrier folding pathways between conformational structures. RNAEAPath guides the construction of folding pathways through the destruction and formation of RNA stacks using various…

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RNA FRABASE
Dataset

RNA FRABASE

An engine with database to search the three-dimensional fragments within 3D RNA…

An engine with database to search the three-dimensional fragments within 3D RNA structures using as an input the sequence(s) and / or secondary structure(s) given in the dot-bracket notation.

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Cartaj
Web
Desktop

Cartaj

Predicts the topological family of three-way RNA junctions from their secondary…

Predicts the topological family of three-way RNA junctions from their secondary structure only. Cartaj is an automated method that works well on single junctions, and is improved either by having…

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alteRNA
Web

alteRNA

Minimizes a linear combination of total free energy and total energy density…

Minimizes a linear combination of total free energy and total energy density using the dynamic programming formulation. alteRNA is an alternative thermodynamic approach to the RNA secondary structure…

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SPARCS
Web

SPARCS Structural Profile Assignment of RNA Coding Sequences

Predicts structured, unstructured and disordered regions in coding RNA…

Predicts structured, unstructured and disordered regions in coding RNA sequences. SPARCS enables to sample uniformly random sequences preserving the encoded protein sequence and the DFs. It provides…

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LocARNAscan
Desktop

LocARNAscan

Computes alignments of a query RNA with a much longer target sequence based on…

Computes alignments of a query RNA with a much longer target sequence based on sequence and structure similarity. LocARNAscan is a scanning variant of LocARNA, a computationally light-weight and very…

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eSBMTools
Desktop

eSBMTools

Assists users in performing and evaluating simulations in the field of…

Assists users in performing and evaluating simulations in the field of structure-based models (SBMs). eSBMTools is organized in modules that can be loaded into Python projects. It can be used at all…

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AveRNA
Web

AveRNA

Provides an ensemble-based RNA secondary structure prediction method. AveRNA…

Provides an ensemble-based RNA secondary structure prediction method. AveRNA can make use of arbitrary secondary structure prediction procedures. In particular, it can be used to combine both maximum…

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Dot-Bracket…
Web

Dot-Bracket Rendering

Provides a RNA secondary structure prediction method based on conditional…

Provides a RNA secondary structure prediction method based on conditional log-linear models (CLLMs). Dot-Bracket Rendering is a method for rendering of dot-bracket structures.

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Mea
Server

Mea Maximum Expected Accuracy

Predicts maximum expected accuracy (MEA) RNA secondary structures from dot…

Predicts maximum expected accuracy (MEA) RNA secondary structures from dot plots of RNAs while correcting the score in dependence of base pair span. Mea is an application that also provides tools to…

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Grammar string
Desktop

Grammar string

Implements a consensus structure derivation tool based on grammar string, a…

Implements a consensus structure derivation tool based on grammar string, a noncoding RNA (ncRNA) secondary structure representation. Grammar string encodes an ncRNA’s sequence and secondary…

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Evofold
Desktop

Evofold

Identifies functional RNA-structure in multiple sequence alignments. Evofold…

Identifies functional RNA-structure in multiple sequence alignments. Evofold makes use of a phylogenetic stochastic context-free grammar (phylo-SCFG) which is a combined probabilistic model of RNA…

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Tfold
Web

Tfold

Allows prediction of non-coding RNA secondary structures. Tfold combines the…

Allows prediction of non-coding RNA secondary structures. Tfold combines the SSCA algorithm and the P-DCFold algorithm. It returns several structures, when there are ‘rival’ stems with close…

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CompaRNA
Dataset

CompaRNA

Provides an automated system for the continuous evaluation of RNA structure…

Provides an automated system for the continuous evaluation of RNA structure prediction methods. The goal of CompaRNA is to provide a ‘blind’ benchmark using experimental data before it becomes…

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RSpredict
Web

RSpredict

An RNA secondary structure prediction tool that works on multiple sequence…

An RNA secondary structure prediction tool that works on multiple sequence alignments.

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Rchange
Desktop

Rchange

Computes energy changes of RNA secondary structures in response to base…

Computes energy changes of RNA secondary structures in response to base mutations. Rchange computes the changes of the ensemble free energy, mean energy and the thermodynamic entropy of RNA secondary…

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RNAstrand
Web
Desktop

RNAstrand

Allows users to determine the reading direction of a multiple sequence…

Allows users to determine the reading direction of a multiple sequence alignment containing evolutionary conserved RNA secondary structure from a ClustalW sequence alignment. RNAstrand uses a support…

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