List of RNA structure prediction software: Wikis

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This list of RNA structure prediction software is a compilation of software tools and web portals used for RNA structure prediction.

Contents

Single sequence secondary structure prediction

Name Description Knots Links References
CentroidFold Secondary structure prediction based on generalized centroid estimator no sourcecode webserver [1]
CONTRAfold Secondary structure prediction method based on conditional log-linear models (CLLMs), a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. no sourcecode webserver [2]
KineFold Folding kinetics of RNA sequences including pseudoknots by including an implementation of the partition function for knots. yes linuxbinary, webserver [3][4]
Mfold MFE RNA structure prediction algorithm. no sourcecode, webserver [5]
Pknots A dynamic programming algorithm for optimal RNA pseudoknot prediction using the nearest neighbour energy model. yes sourcecode [6]
PknotsRG A dynamic programming algorithm for the prediction of a restricted class of RNA pseudoknots. yes sourcecode, webserver [7]
RNAfold MFE RNA structure prediction algorithm. Includes an implementation of the partition function for computing basepair probabilities and circular RNA folding. no sourcecode, webserver

[5][8][9][10][11][12]

RNAshapes MFE RNA structure prediction based on abstract shapes. Shape abstraction retains adjacency and nesting of structural features, but disregards helix lengths, thus reduces the number of suboptimal solutions without losing significant information. Furthermore, shapes represent classes of structures for which probabilities based on Boltzmann-weighted energies can be computed. no source & binaries, webserver [13][14]
RNAstructure A program to predict lowest free energy structures and base pair probabilities for RNA or DNA sequences. Structure prediction can be constrained using experimental data, including SHAPE, enzymatic cleavage, and chemical modification accessibility. Graphical user interfaces are available for Windows and for Mac OS-X/Linux. Programs are also available for use with Unix-style text interfaces. Additionally, a C++ class library is available. no source & binaries

[15][16]

Sfold Statistical sampling of all possible structures. The sampling is weighted by partition function probabilities. no webserver [17][18][19][20]
UNAFold The UNAFold software package is an integrated collection of programs that simulate folding, hybridization, and melting pathways for one or two single-stranded nucleic acid sequences. no sourcecode [21]
*Knots: Pseudoknot prediction, <yes|no>.

Single sequence tertiary structure prediction

Name Description Knots Links References
BARNACLE A Python library for the probabilistic sampling of RNA structures that are compatible with a given nucleotide sequence and that are RNA-like on a local length scale. yes sourcecode [22]
FARNA Automated de novo prediction of native-like RNA tertiary structures . yes sourcecode [23]
iFoldRNA three-dimensional RNA structure prediction and folding  ? webserver [24]
MC-Fold MC-Sym Pipeline Thermodynamics and Nucleotide cyclic motifs for RNA structure prediction algorithm. 2D and 3D structures. yes sourcecode, webserver [25]
NAST Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters  ? sourcecode [26]
*Knots: Pseudoknot prediction, <yes|no>.

Comparative methods

The single sequence methods mentioned above have a difficult job detecting a small sample of reasonable secondary structures from a large space of possible structures. A good way to reduce the size of the space is to use evolutionary approaches. Structures that have been conserved by evolution are far more likely to be the functional form. The methods below use this approach.

Name Description Number of sequences Alignment Structure Knots Link References
Carnac Comparative analysis combined with MFE folding. any no yes no sourcecode, webserver [27][28]
CMfinder an expectation maximization algorithm using covariance models for motif description. Uses heuristics for effective motif search, and a Bayesian framework for structure prediction combining folding energy and sequence covariation. 3\le seqs \le60 yes yes no sourcecode, webserver [29]
CONSAN implements a pinned Sankoff algorithm for simultaneous pairwise RNA alignment and consensus structure prediction. 2 yes yes no sourcecode [30]
Dynalign an algorithm that improves the accuracy of structure prediction by combining free energy minimization and comparative sequence analysis to find a low free energy structure common to two sequences without requiring any sequence identity. 2 yes yes no sourcecode [31][32][33]
FoldalignM A multiple RNA structural RNA alignment method, to a large extend based on the PMcomp program. any yes yes no sourcecode [34]
KNetFold Computes a consensus RNA secondary structure from an RNA sequence alignment based on machine learning. any input yes yes linuxbinary, webserver [35]
LARA Produce a global fold and alignment of ncRNA families using integer linear programming and Lagrangian relaxation. any yes yes no sourcecode [36]
LocaRNA LocaRNA is the successor of PMcomp with an improved time complexity. It is a variant of Sankoff's algorithm for simultaneous folding and alignment, which takes as input pre-computed base pair probability matrices from McCaskill's algorithm as produced by RNAfold -p. Thus the method can also be viewed as way to compare base pair probability matrices. any yes yes no sourcecode [37]
MASTR A sampling approach using Markov chain Monte Carlo in a simulated annealing framework, where both structure and alignment is optimized by making small local changes. The score combines the log-likelihood of the alignment, a covariation term and the basepair probabilities. any yes yes no sourcecode [38][39]
Murlet a multiple alignment tool for RNA sequences using iterative alignment based on Sankoff's algorithm with sharply reduced computational time and memory. any yes yes no webserver [40]
MXSCARNA a multiple alignment tool for RNA sequences using progressive alignment based on pairwise structural alignment algorithm of SCARNA. any yes yes no webserver sourcecode [41]
PARTS A method for joint prediction of alignment and common secondary structures of two RNA sequences using a probabilistic model based on pseudo free energies obtained from precomputed base pairing and alignment probabilities. 2 yes yes no sourcecode [42]
Pfold Folds alignments using a SCFG trained on rRNA alignments. \le40 input yes no webserver [43][44]
PMcomp/PMmulti PMcomp is a variant of Sankoff's algorithm for simultaneous folding and alignment, which takes as input pre-computed base pair probability matrices from McCaskill's algorithm as produced by RNAfold -p. Thus the method can also be viewed as way to compare base pair probability matrices. PMmulti is a wrapper program that does progressive multiple alignments by repeatedly calling pmcomp 2\le seqs \le6 yes yes no sourcecode, webserver [45]
R-COFFEE uses RNAlpfold to compute the secondary structure of the provided sequences. A modified version of T-Coffee is then used to compute the multiple sequence alignment having the best agreement with the sequences and the structures. R-Coffee can be combined with any existing sequence alignment method. any yes yes no sourcecode, webserver [46][47]
RNAalifold Folds precomputed alignments using a combination of free-energy and a covariation measures. Ships with the Vienna package. any input yes no homepage [8][48]
RNAcast enumerates the near-optimal abstract shape space, and predicts as the consensus an abstract shape common to all sequences, and for each sequence, the thermodynamically best structure which has this abstract shape. any no yes no sourcecode, webserver [49]
RNAforester Compare and align RNA secondary structures via a "forest alignment" approach. any yes input no sourcecode, webserver [50][51]
RNAmine Frequent stem pattern miner from unaligned RNA sequences is a software tool to extract the structural motifs from a set of RNA sequences. any no yes no webserver [52]
RNASampler A probabilistic sampling approach that combines intrasequence base pairing probabilities with intersequence base alignment probabilities. This is used to sample possible stems for each sequence and compare these stems between all pairs of sequences to predict a consensus structure for two sequences. The method is extended to predict the common structure conserved among multiple sequences by using a consistency-based score that incorporates information from all the pairwise structural alignments. any yes yes yes sourcecode [53]
SCARNA Stem Candidate Aligner for RNA (Scarna) is a fast, convenient tool for structural alignment of a pair of RNA sequences. It aligns two RNA sequences and calculates the similarities of them, based on the estimated common secondary structures. It works even for pseudoknotted secondary structures. 2 yes yes no webserver [54]
SimulFold simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework. any yes yes yes sourcecode [55]
Stemloc a program for pairwise RNA structural alignment based on probabilistic models of RNA structure known as Pair stochastic context-free grammars. any yes yes no sourcecode [56]
StrAl an alignment tool designed to provide multiple alignments of non-coding RNAs following a fast progressive strategy. It combines the thermodynamic base pairing information derived from RNAfold calculations in the form of base pairing probability vectors with the information of the primary sequence. \le50 yes no no sourcecode, webserver [57]
WAR a webserver that makes it possible to simultaneously use a number of state of the art methods for performing multiple alignment and secondary structure prediction for noncoding RNA sequences. 2\le seqs \le50 yes yes no webserver [58]
Xrate a program for analysis of multiple sequence alignments using phylogenetic grammars, that may be viewed as a flexible generalization of the "Pfold" program. any yes yes no sourcecode [59]
* Number of sequences: <any|num>. * Alignment: predicts an alignment, <input|yes|no>. * Structure: predicts structure, <input|yes|no>. * Knots: pseudoknot prediction, <yes|no>.

Inter molecular interactions: RNA-RNA

Many ncRNAs function by binding to other RNAs. For example, miRNAs regulate protein coding gene expression by binding to 3' UTRs, small nucleolar RNAs guide post-transcriptional modifications by binding to rRNA, U4 spliceosomal RNA and U6 spliceosomal RNA bind to each other forming part of the spliceosome and many small bacterial RNAs regulate gene expression by antisense interactions Eg. GcvB, OxyS and RyhB.

Name Description Intra-molecular structure Comparative Link References
NUPACK Computes the full unpseudoknotted partition function of interacting strands in dilute solution. Calculates the concentrations, mfes, and base-pairing probabilities of the ordered complexes below a certain complexity. Also computes the partition function and basepairing of single strands including a class of pseudoknotted structures. Also enables design of ordered complexes. yes no NUPACK [60]
OligoWalk/RNAstructure Predicts bimolecular secondary structures with and without intramolecular strucure. Also predicts the hybridization affinity of a short nucleic acid to an RNA target. yes no [1] [61]
piRNA calculates the partition function and thermodynamics of RNA-RNA interactions. It considers all possible joint secondary structure of two interacting nucleic acids that do not contain pseudoknots, interaction pseudoknots, or zigzags. yes no linuxbinary [62]
RNAaliduplex Based upon RNAduplex with bonuses for covarying sites no yes sourcecode [8]
RNAcofold works much like RNAfold, but allows to specify two RNA sequences which are then allowed to form a dimer structure. yes no sourcecode [8][63]
RNAduplex computes optimal and suboptimal secondary structures for hybridization. The calculation is simplified by allowing only inter-molecular base pairs. no no sourcecode [8]
RNAhybrid a tool for finding the minimum free energy hybridisation of a long and a short RNA. no no sourcecode, webserver [64][65]
RNAup calculates the thermodynamics of RNA-RNA interactions. RNA-RNA binding is decomposed into two stages. (1) First the probability that a sequence interval (e.g. a binding site) remains unpaired is computed. (2) Then the binding energy given that the binding site is unpaired is calculated as the optimum over all possible types of bindings. yes no sourcecode [8][66]
*

Inter molecular interactions: MicroRNA:UTR

MicroRNAs regulate protein coding gene expression by binding to 3' UTRs, there are tools specifically designed for predicting these interactions.

Name Description Species Specific Intra-molecular structure Comparative Link References
MicroTar An animal miRNA target prediction tool based on miRNA-target complementarity and thermodynamic data. no no no sourcecode [67]
miTarget microRNA target gene prediction using a support vector machine. no no no webserver [68]
PicTar Combinatorial microRNA target predictions. 8 vertebrates no yes predictions [69]
PITA Incorporates the role of target-site accessibility, as determined by base-pairing interactions within the mRNA, in microRNA target recognition. no yes no executable, webserver, predictions [70]
RNA22 First finds putative microRNA binding sites in the sequence of interest, then identifies the targeting microRNA. no no no webserver [71]
RNAhybrid a tool for finding the minimum free energy hybridisation of a long and a short RNA. no no no sourcecode, webserver [64][65]
TargetScan Predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA. Predictions are ranked using site number, site type, and site context, which includes factors that influence target-site accessibility. vertebrates, flies, nematodes evaluated indirectly yes sourcecode, webserver [72][73][74]
Sylamer Sylamer is a method for finding significantly over or under-represented words in sequences according to a sorted gene list. Typically it is used to find significant enrichment or depletion of microRNA or siRNA seed sequences from microarray expression data. no no no sourcecode [75]
*

ncRNA gene prediction software

Name Description Number of sequences Alignment Structure Link References
Alifoldz Assessing a multiple sequence alignment for the existence of an unusual stable and conserved RNA secondary structure. any input yes sourcecode [76]
EvoFold a comparative method for identifying functional RNA structures in multiple-sequence alignments. It is based on a probabilistic model-construction called a phylo-SCFG and exploits the characteristic differences of the substitution process in stem-pairing and unpaired regions to make its predictions. any input yes linuxbinary [77]
MSARi heuristic search for statistically significant conservation of RNA secondary structure in deep multiple sequence alignments. any input yes sourcecode [78]
QRNA This is the code from Elena Rivas that accompanies a submitted manuscript "Noncoding RNA gene detection using camparative sequence analysis". QRNA uses comparative genome sequence analysis to detect conserved RNA secondary structures, including both ncRNA genes and cis-regulatory RNA structures. 2 input yes sourcecode [79][80]
RNAz program for predicting structurally conserved and thermodynamic stable RNA secondary structures in multiple sequence alignments. It can be used in genome wide screens to detect functional RNA structures, as found in noncoding RNAs and cis-acting regulatory elements of mRNAs. any input yes sourcecode, webserver [81][82][83]
Xrate a program for analysis of multiple sequence alignments using phylogenetic grammars, that may be viewed as a flexible generalization of the "Evofold" program. any yes yes sourcecode [59]
* Number of sequences: <any|num>. * Alignment: predicts an alignment, <input|yes|no>. * Structure: predicts structure, <input|yes|no>.

Family specific gene prediction software

Name Description Family Link References
miRNAminer Given a search query, candidate homologs are identified using BLAST search and then tested for their known miRNA properties, such as secondary structure, energy, alignment and conservation, in order to assess their fidelity. MicroRNA webserver [84]
RISCbinder Prediction of guide strand of microRNAs. Mature miRNA webserver [85]
RNAmicro A SVM-based approach that, in conjunction with a non-stringent filter for consensus secondary structures, is capable of recognizing microRNA precursors in multiple sequence alignments. MicroRNA homepage [86]
RNAmmer RNAmmer uses HMMER to annotate rRNA genes in genome sequences. Profiles were built using alignments from the European ribosomal RNA database[87] and the 5S Ribosomal RNA Database[88]. rRNA webserver source [89]
SnoReport Uses a combination of RNA secondary structure prediction and machine learning that is designed to recognize the two major classes of snoRNAs, box C/D and box H/ACA snoRNAs, among ncRNA candidate sequences. snoRNA sourcecode [90]
SnoScan Search for C/D box methylation guide snoRNA genes in a genomic sequence. C/D box snoRNA sourcecode, webserver [91][92]
tRNAscan-SE a program for the detection of transfer RNA genes in genomic sequence. tRNA sourcecode, webserver [92][93]
.

RNA homology search software

Name Description Link References
ERPIN "Easy RNA Profile IdentificatioN" is an RNA motif search program reads a sequence alignement and secondary structure, and automatically infers a statistical "secondary structure profile" (SSP). An original Dynamic Programming algorithm then matches this SSP onto any target database, finding solutions and their associated scores. sourcecode webserver [94][95][96]
Infernal "INFERence of RNA ALignment" is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). sourcecode [97][98][99]
PHMMTS "pair hidden Markov models on tree structures" is an extension of pair hidden Markov models defined on alignments of trees. sourcecode, webserver [100]
RaveNnA A slow and rigorous or fast and heuristic sequence-based filter for covariance models. sourcecode [101][102]
RSEARCH Takes a single RNA sequence with its secondary structure and utilizes a local alignment algorithm to search a database for homologous RNAs. sourcecode [103]
.

Benchmarks

Name Description Structure Alignment Phylogeny Links References
BRalibase I A comprehensive comparison of comparative RNA structure prediction approaches yes no no data [104]
BRalibase II A benchmark of multiple sequence alignment programs upon structural RNAs no yes no data [105]
BRalibase III A critical assessment of the performance of homology search methods on noncoding RNA no yes no data [106]
* Alignment: benchmarks alignment tools <yes|no>. * Structure: benchmarks structure prediction tools <yes|no>.

Viewers/Editors

Name Description Alignment Structure Link References
4sale A tool for Synchronous RNA Sequence and Secondary Structure Alignment and Editing yes yes sourcecode [107]
Colorstock, SScolor, Raton Colorstock, a command-line script using ANSI terminal color; SScolor, a Perl script that generates static HTML pages; and Raton, an AJAX web application generating dynamic HTML. Each tool can be used to color RNA alignments by secondary structure and to visually highlight compensatory mutations in stems. yes yes sourcecode [108]
RALEE a major mode for the Emacs text editor. It provides functionality to aid the viewing and editing of multiple sequence alignments of structured RNAs. yes yes sourcecode [109]
SARSE A graphical sequence editor for working with structural alignments of RNA. yes yes sourcecode [110]
* Alignment: view and edit an alignment, <yes|no>. * Structure: view and edit structure, <yes|no>

See also

References

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