0 we have enabled G-Quadruplex prediction support into RNAfold, RNAcofold, RNALfold, RNAalifold, RNAeval and RNAplot. Nucleic Acids Res. Calculate the conserved structures of three or more unaligned sequences using iteratively refined partition functions. THE RNAfold SERVER. 4. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities. We perform discrete molecular dynamics simulations of RNA using coarse-grained structural models (three-beads/residue). The Bimolecular Fold server allows formation of intramolecular pairs if desired, but the DuplexFold server does not allow formation of intramolecular pairs . 05 - 21 - 2012. LinearFold-V (the LinearFold implementation of the Vienna RNAfold model) also outperforms RNAfold with significant improvements in PPV on two families (SRP and 16S rRNA), and both PPV/sensitivity on one family (Group I Intron). 1 Implementation. The minimum free energy structure found is at the top left of the graph. Font::TTf already installed, nothing to do. perl install. Then typing. ) parallel. conda install. This makes it easier for users to make the transition to locally installed. RNAfold. ps. If no name is provided, the system clock time of the web server when the job is submitted will be taken as the job name. RNA secondary structure: The basics. DESCRIPTION. It does this by generating pairwise alignments between sequences using a hidden markov model. The original paper has been cited over 2000 times. TurboFold. iFoldRNA rapidly explores RNA conformations. [Supplementary Material] [Additional. The large gap between the number of sequences and the experimentally determined. Pappu, in Methods in Enzymology, 2009 Abstract. Computational prediction is a mainstream approach for predicting RNA secondary structure. This single tool not only displays the sequence/structural consensus alignments for each RNA family, according to Rfam database but also provides a taxonomic overview for each assigned functional RNA. Using this server, it is possible to calculate the folding nucleus for RNA molecules with known 3D structures-including. DNA mfold server. For the folding it makes use of a very realistic energy model for RNAs as it is by RNAfold of the Vienna RNA package (or Zuker's mfold). Fax: 314. Hi, I am having problem while installing mirdeep2. The Vfold server offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b) three-dimensional structure from the two-dimensional structure and the sequence, and (c) folding thermodynamics (heat capacity melting curve) from the sequence. The RNA molecule is an ordered sequence of nucleotides that contain 1 of the 4 bases: adenine (A), cytosine (C), guanine (G), and uracil (U), arranged in the 5′ to 3′ direction. Ribonucleic acid (RNA) molecules play vital roles in numerous important biological functions such as catalysis and gene regulation. Table 3 indicates that RNAfold and MXfold2 with thermodynamic regularization can calculate folding scores that are highly correlated with true free energy estimates, at least for sequences for which secondary structures can be predicted with high accuracy. DNA mfold server. All 1D features (one-hot encoding and PSSM, L × 4 ) were converted into 2D features of size L × 16 using the outer-concatenation function as described in RaptorX-Contact ( Wang et al. Significant improvements have been made in the efficiency and accuracy of RNA 3D structure prediction methods in recent years; however, many tools developed in the field stay exclusive to only a few bioinformatic groups. CoFold is a thermodynamics-based RNA secondary structure folding algorithm that takes co-transcriptional folding in account. Multiple native-like RNA topologies and the corresponding relative free energy values are accessible from the iFoldRNA server. Here is an example that adds a theophylline binding motif. 1093/nar/gkh449. We would like to show you a description here but the site won’t allow us. 3 RESULTS. Current limits are 7,500 nt for partition function calculations and 10,000 nt for minimum free. Using R2D2 to Understand RNA Folding. The calculation time scales according to O(N 3), where N is the length of the sequence. The mfold web server is one of the oldest web servers in computational molecular biology. e. A separate program, PlotFold, reads these energy matrices and displays representative secondary structures. Generally speaking, energy-based methods have been at the forefront of RNA secondary structure. RNAbracket = rnafold (Seq) predicts and returns the secondary structure associated with the minimum free energy for the RNA sequence, Seq, using the thermodynamic nearest-neighbor approach. However, experimental determination of the atomic structures is laborious and technically difficult. As predicted by RNAfold 44, a nearly perfect dsRNA structure is formed between edited region at intron 8 and regions 4 and 5 at intron 9, with all three ADAR1-regulated sites in stem region. The default behavior of RNAfold is to read input from stdin or the file(s) that follow(s) the RNAfold command. pl and utils/parse_blastn_local. If this is not the case, the path to RNAFold can be manually entered in selfcontain. The mfold Web Server. It first predicts 2D structures using the Vfold2D model [2-7] and then predicts 3D structures based on the predicted 2D structures using the Vfold3D [8] and VfoldLA [9] models. As expected, the new version of RNAfold performs better than the old one. The first centers on the most appropriate biophysical. Even with the exclusion of pseudoknots, the number of possible secondary structures of a long RNA sequence is enormous (∼1. For example, the output file created in the MFold example session requires approximately 0. The Kinefold web server provides a web interface for stochastic folding simulations of nucleic acids on second to minute molecular time scales. We maintain a reference manual describing the. Abstract. All non-alphabet characters will be removed. FASTA format may be used. Fold and Fold-smp. Calculate the partition function and base pairing probability matrix in addition to the minimum free energy (MFE) structure. RNAfold –shapeMethod = “W” was used to obtain in vivo DMS soft-constrained structures (this method is referred to as ‘RNAfold Soft Constraints’ in the figures and text) using τ / σ = 1 as suggested by the analysis in the original RNA folding with soft constraints paper . aj03 commented on Nov 18, 2016. LinearFold, in contrast, uses ) space thanks to left-to-right beam search, and is the first )-space algorithm to be able to predict base pairs of unbounded distance. Eq (33)] by running RNAfold -p -T 37. There exists by now ample experimental and theoretical evidence that the process of structure formati. This should get you familiar with the input and output format as well as the graphical output produced. The Vfold3D/VfoldLA methods are based. Each binding site was located inside a window of. This algorithm is the second, and much larger, test case for ADPfusion. RNAfold from the ViennaRNA package [19] is the most commonly used program to predict circRNA structure in silico [13], [14]. RNAfold and QGRS-Mapper 14 both predict the same RNA G4 with three G-tetrads for the wild-type sequence. wustl. RNA folding and applications. The secondary structure together with the sequence can be passed on to the RNAeval web server, which gives a detailed thermodynamic description according to the. Since dimer formation is concentration dependent, RNAcofold can be used to compute equilibrium concentrations for all five monomer and (homo/hetero)-dimer species, given input concentrations for the monomers (see the man page for details). If the template is missing, a distance-geometry-based loop building method can be used to build the SSE ab initio. 86 N ) ( 20 ), yielding. along the lines of Eddy (2014) , or the application to. 14) is used for predicting and drawing the secondary structure of mRNA sequence, and calculating the MFE of secondary structures. : RNA secondary structure prediction using deep learning with thermodynamic integration, Nat Commun 12, 941 (2021. A webserver for mfold can be accessed here. Tool for finding the minimum free energy hybridization of a long and a short RNA. Introduction. Comparison of the secondary structure energy predictions between G4Boost and RNAfold yielded an RMSE score of 16. The main routines for 3dRNA/DNA is: Break the given secondary structure into smallest secondary elements (SSEs). a Precision-recall curves on the independent test set TS1 by initial training (SPOT-RNA-IT, the green dashed line), direct training (SPOT-RNA-DT, the blue dot-dashed line), and transfer learning (SPOT-RNA, the solid magenta. The required changes to the folding recursions and technical details of handling both hard and soft constraints in ViennaRNA will be. Abstract. The mfold Web Server. gz or mfold-3. This contribution describes a new set of web servers to provide its functionality. RNAfold web server is a tool that calculates the optimal or minimum free energy structure of single stranded RNA or DNA sequences. RNAstructure is a software package for RNA secondary structure prediction and analysis. Major changes in the structure of the standard energy model, the Turner 2004 parameters, the pervasive use of multi-core CPUs, and an increasing number of algorithmic variants prompted a. Apart from a few positions, no significant difference was observed in the prediction of S protein B cell and T cell epitopes of these two variants. To see a demo of the functionality click on 'Add Molecule' and then 'Submit'. [External] RNA secondary structure tools. Mfold web server for nucleic acid folding and hybridization prediction. Because it uses only atomic coordinates as inputs and incorporates no RNA-specific information, this approach is applicable to diverse problems in structural biology, chemistry, materials science, and beyond. RNAs also play essential roles in gene regulation via riboswitches, microRNAs and lncRNAs. Here, consistent with the requirement of DRfold, both RNAfold and PETfold are configured with sequence input only. See for details. mfold is the most widely used tool for RNA secondary structure prediction based on thermodynamic methods [1]. Here, we propose a deep learning-based method, called UFold, for RNA secondary structure prediction, trained directly on annotated data and base-pairing rules. Welcome to the ProbKnot Web Server. Introduction. FASTA format may be used. 29, 1034-1046. The restriction on length of input sequences is due to the limits set by RNAfold and RPISeq programs used in backend processing of server. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. Using this parameter the user can specify input file names where data is read from. 35 megabytes of disk storage. Create force-directed graphs of RNA secondary structures. Finally, Frnakenstein is a recent Python program that calls Vienna RNA Package RNAfold and RNAeval within a genetic algorithm to evolve collection of RNA sequences to have low energy structures with respect to one or more target structures (as solution sequences are compatible with than one target structure, structural compatibility. Detailed output, in the form of structure plots. edu. M. It has been in continuous operation since the fall of 1995 when it was introduced at Washington University's School of Medicine. Plots are augmented by a special colouring schema that indicates compensatory mutations. 41 and an R2. The developers used the RNAfold algorithm to generate the secondary structure and point diagrams with pairing probabilities and applied MirTarget2 algorithm to predict miRNA seeds. The web server offers RNA secondary structure prediction, including free energy minimization, maximum expected accuracy structure prediction and pseudoknot. The program reads RNA sequences, calculates their minimum. , CONTRAfold 14, CentroidFold 15. A convenience function allows one to specify a hairping/interior loop motif where a ligand is binding with a particular binding free energy dG. Ding, Y. The hybridization is performed in a kind of domain mode, ie. This algorithm leverages the integration of structure templates of helices, loops, and other motifs from known RNA 3D structures. RNAfold 2. The RNAsoft suite of programs provides tools for predicting the secondary structure of a pair of DNA or RNA molecules, testing that combinatorial tag sets of DNA and RNA molecules have no unwanted secondary structure and designing RNA strands that fold to a given input secondary structure. In case of issue regarding installation of these predictors, please refer to more specific and detailed guide for ViennaRNA and SPOT-RNA . cores: Integer. RNAfold (version 2. 99], then the resulting entropy for the 98 nt. . Motivation: To gain insight into how biopolymers fold as quickly as they do, it is useful to determine which structural elements limit the rate of RNA/protein folding. A preliminary version of the ViennaRNA Package implementing RNA/DNA hybrid support can be found here. 5°C. However, it is known that due to several reasons, such as interactions with proteins or other RNAs and processing of RNAs, the. 6 of mfold contains the non-interactive programs from mfold_util version 4. FASTA format may be used. Sequences: Enter one or more sequences in FASTA format. 2D. 4. Paste or type your first sequence here:RNAfold, rather than SPOT-RNA, was employed for generating consensus secondary structure (CSS) for RNAcmap. 1: Decomposition of an RNA. And then run the following codes: $ python ufold_predict. The user can adjust the temperature and 5 other parameters. 0068 has been tuned to best fit the tabulated thermodynamic parameters for short loops ( 34, 35)]. We discovered that CONTRAfold 2, which inferred thermodynamic parameters by feature representation in datasets of natural RNA secondary structures, performed. The RNAfold server output contains the predicted MFE secondary structure in the usual dot-bracket notation, additionally mfold-style Connect (ct) files ( 9) can be downloaded. E. , RNAfold 11, RNAstructure 12, and RNAshapes 13) or by machine learning (e. The output is similar to that of the RNAfold server, but also features a structure annotated alignment. j Secondary structure of G-rich region detected by rG4-seq (in g) and flanking sequences on AT3G23450, predicted using Vienna RNAfold. The eps format of melting curve is generated by Gnuplot. A. We predicted the secondary structure of 20,034 shRNA variants using RNAfold 62. The abbreviated name, ‘mfold web server’, describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. (This is also achieved with RNAfold, option -C. The name is derived from "Unified Nucleic Acid Folding". C Schematic diagram for RIP-qPCR. The dot-bracket structure, obtained from RNAfold, was converted into custom-designed structures in which each nt was. The submission of sequence(s) invokes the accessary. The three-dimensional (3D) structures of Ribonucleic acid (RNA) molecules are essential to understanding their various and important biological functions. HotKnots predicts RNA secondary structures with pseudoknots. Results: Inspired by the success of our recent LinearFold algorithm that predicts the approximate minimum free energy structure in linear time, we design a similar linear-time heuristic algorithm, LinearPartition, to approximate the partition function and base-pairing probabilities, which is shown to be orders of magnitude faster than Vienna. txt --batch < sequences. Amongst other things, our implementations allow you to: predict minimum free energy secondary structures. A multiplicative factor α, corresponding to the ‘confinement’ cost each time a loop is formed, is added for each helix on the structure [α = 0. g. All non-alphabet characters will be removed. a Calculations were performed on a computer with a 3. A job name can be entered in the text box in the first step. Comparison of the secondary structure energy predictions between G4Boost and RNAfold yielded an RMSE score of 16. It is no longer necessary to download and install mfold_util separately. This single tool not only displays the sequence/structural consensus alignments for each RNA family, according to Rfam database but also provides a taxonomic overview for each assigned functional RNA. Simply paste or upload your sequence below and click Proceed. See examples of tRNA secondary structure. Figure 3: Examples of siRNA target sites (red) on the corresponding mRNA secondary structure predicted using RNAfold. pl from HHsuite-github-repo; utils/getpssm. The new RNAalifold version with better gap character handling. Click the "View and edit calculation parameters" button in the side toolbar to view the settings used to calculate the displayed structures. . Especially, please read the section of "Choosing iFoldRNA. 1. Office: 314. RNA2DMut is a user-friendly tool that automates the folding of mutants (using the popular RNAfold algorithm [Hofacker 2003; Lorenz et al. Executable programs shipped with the ViennaRNA Package are documented by corresponding man pages, use e. e. However, these methods cannot accurately predict secondary structures withRNAhybrid (biotools:rnahybrid) ID Verified. 2. RNAfold web server is a tool that calculates the optimal or minimum free energy structure of single stranded RNA or DNA sequences. - Rnafold (1) output files can also be merged with existing sequence files given that both files designate the same RNA sequence. The mfold web server is one of the oldest web servers in computational molecular biology. Structures. In general, Mfold, RNAfold, and MXfold2 seem to currently be the best choice for the ssNAs secondary structure prediction, although they still show some limits linked to specific structural motifs. (optional) You may: force bases i,i+1,. First-principle algorithmic approaches to this task are challenging because existing models of the folding process are inaccurate, and even if a perfect model existed, finding an optimal solution. The simulation of immune responses to the mRNA vaccine construct was performed using C-ImmSim. By default this viewer is only shown when an oligo sequence is selected. 4. SPOT-RNA: RNA Secondary Structure Prediction using an Ensemble of Two-dimensional Deep Neural Networks and Transfer Learning. 1. [External]Installation of RNAfold will take 15-20 mins and 2-3 mins for SPOT-RNA. Enter the sequence to be folded in the box below. In recent years, several. This chapter describes a recently developed RNA structure prediction software, Vfold, a virtual bond-based RNA folding model. FASTA format may be used. g. An RNA manipulation library. Welcome to iFoldRNA Ver 2. Learn how to use the rnafold and rnaplot functions to predict and plot the secondary structure of an RNA sequence using the nearest-neighbor thermodynamic model. Enter the sequence to be folded in the box below. Fig. For the alignment it features RIBOSUM-like similarity scoring and realistic gap cost. The Fold server also allows specification of SHAPE data, namely, a SHAPE constraints file, SHAPE intercept, and SHAPE slope. ∆LFE analysis reveals that on average for all genes, an RTS is present and localized downstream of stop codons across (b) E. 0, RNAfold 1. 8. This shows an example secondary structure. Note that this server does not just output the. Fold-smp is a parallel processing version for use on multi-core computers, built using. E Schematic diagram for RNA pull down. Ribosomal RNA analysis. Delivery (courier): 4240 Duncan Avenue - Suite 110. "RNA is a really important piece of diagnostic and therapeutic design. 0-manual. Both a library version and an executable are created. Displayed are secondary structures predicted by various methods, such as MFE, ensemble centroid, MEA structure, as well as suboptimal structures obtained from stochastic backtracking (marked by S), and the 5 best suboptimals sensu Zuker (marked by Z), all implemented in the programs RNAfold, and RNAsubopt of the ViennaRNA. Current Protocols is a comprehensive journal for protocols and overviews covering experimental design, scientific research methods and analyses across life sciences. RNAfold web server - Motivation: To gain insight into how biopolymers fold as quickly as they do, it is useful to determine which structural elements limit the rate of RNA/protein folding. Anyone with the URL may view a particular set of results. This model assumes that the process of RNA folding from the random coil state to full structure is staged and in every stage of. Ding, Y. Background The understanding of the importance of RNA has dramatically changed over recent years. To provide an automatic prediction method, we now offer one easy-to-use web server using only RNA tertiary structures as input information. This basic set consists of loop-type dependent hard constraints for single nucleotides and. Especially SHAPE data were successfully integrated into thermodynamic algorithms, providing not only the. The tool is intended for designers of RNA molecules with particular structural or functional properties. This has been shown to significantly improve the state-of-art in terms of prediction accuracy, especially for long sequences greater than 1000 nt in length. RNA2DMut can facilitate the design of mutations to disrupt. The main secondary structure prediction tool is RNAfold, which computes the minimum free energy (MFE) and backtraces an optimal secondary structure. 7. RNA is a single stranded molecule, but it is still capable of forming internal loops that can be stabilized by base pairing, just like its famously double-stranded parent, DNA. The functions of RNAs are strongly coupled to their structures. 1. UFold is a deep learning-based method for predicting RNA secondary structure from nucleotide sequences, trained on annotated data and base-pairing rules. 2 . The Bimolecular Fold server allows formation of intramolecular pairs if desired, but the DuplexFold server does not allow formation of. Note that when using RNAfold, it is essential to use ––betaScale; indeed, if one attempts to compute the entropy using Eq (34) where expected energy is computed from Eq (32) [resp. 8 , and RNAstructure 5. When the base pairing probability matrix is calculated by symbols ,, [ { } ( ) are used for bases that are essentially unpaired, weakly paired, strongly paired without preferred direction, weakly upstream (downstream) paired, and strongly upstream (downstream) paired, respectively. 1/282-335 using the Turner’99 parameters (left panel of Figure 1, left image),. RNA Folding Form V2. g. The package is a C code library that includes several stand-alone programs. 3–0. ViennaRNA RNAfold v2, MFE variant using the ADPfusion library. The input sequence is limited to 10–500 nt long. It also designs an RNA sequence that folds to a. 12 were all run locally on an HPC cluster using command line defaults. However, experimental determination of RNA 3D structures is laborious and technically challenging, leading to the huge gap between the number of sequences and the availability of RNA structures. randfold already installed, nothing to do. The abbreviated name, 'mfold web server', describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The EternaBench dataset of synthetic RNA constructs was used to directly compare RNA secondary structure prediction software packages on ensemble-oriented prediction tasks and used to train the. Here, we pose three prominent questions for the field that are at the forefront of our understanding of the importance of RNA folding dynamics for RNA function. g. GAAT-N6-GAAT) and inverted (GAAT-N6-ATTC) repeats. Finally, Frnakenstein is a recent Python program that calls Vienna RNA Package RNAfold and RNAeval within a genetic algorithm to evolve collection of RNA sequences to have low energy structures with respect to one or more target structures (as solution sequences are compatible with than one target structure, structural compatibility. The ViennaRNA Package is a set of standalone programs and libraries used for prediction and analysis of RNA secondary structures. (or) Upload SNP file:RNAs also play essential roles in gene regulation via riboswitches, microRNAs and lncRNAs. The mRNA secondary structure was predicted through the RNAfold. Using. We implement "RNAfold v2" in the MFE variant using "-d2" dangles. Tracks are shown for replicate 1; eCLIP and KD–RNA-seq were performed in biological duplicate with similar results. 286. 0 web server for the users. For illustration, we use the yybP-ykoY. It consists of three CGI scripts equivalent to the RNAfold, RNAalifold and RNAinverse command line programs, respectively. calculate the partition function for the ensemble of structures. RNA folding and binding reactions are mediated by interactions with ions that make up the surrounding aqueous electrolytic milieu. 可能是出图最美的核酸二级结构预测工具. For each sequence, the MFE secondary structure was calculated with RNAfold 2. g. . Thermodynamic methods, such as RNAfold or Mfold , employ a dynamic programming algorithm to find the thermodynamically most stable secondary structure by minimizing the free energy of the folded molecule. A wide variety of constraints can be applied, including, but not limited to, pairing restraints, modifications, and addition of SHAPE data. 5). This basic set consists of loop-type dependent hard constraints for single nucleotides and. We evaluate our sys-tems on a diverse dataset of RNA sequences with well-established structures, and show that while being substantially more efficient,RNAstructure Command Line HelpFold and Fold-smp. In all our test cases, this alignment was. The mfold software is freely accessible and can be downloaded from here. All use a nearest neighbor energy model and a variant of Zuker's dynamic programming algorithm. Quikfold. The Fold server allows specification of a folding constraints file if folding should be restricted in some way. To get more information on the meaning of the options click the symbols. These methods train alternative parameters to the thermodynamic parameters by taking a large number of pairs of RNA sequences and. Inset shows RNA secondary structure prediction (RNAfold) for the indicated region. Availability and implementation: The capability for SHAPE directed RNA folding is part of the upcoming release of the ViennaRNA Package 2. Recently, RNA secondary structure prediction methods based on machine learning have also been developed. RNAfold reads RNA sequences from stdin, calculates their minimum free energy (mfe) structure and prints to stdout the mfe structure in bracket notation and its free energy. Background: To understand an RNA sequence's mechanism of action, the structure must be known. Particularly, reasonably accurate. Note that this server does not just output the structure with a minimum free. an alignment tool designed to provide multiple alignments of non-coding RNAs following a fast progressive strategy. Zuker. The most significant structural elements within the motif are shown within the. RNA folding is the process by which a linear ribonucleic acid (RNA) molecule acquires secondary structure through intra-molecular interactions. However, experimental determination of RNA 3D structures is laborious and technically challenging, leading to the huge gap between the number of sequences and the availability of RNA structures. RNAfold is also executed in with “–enforceConstraint” where the constraints are enforced. You can test the server using these sample sequences. 6. 1 computed by RNAfold -p" 2011 Structure Prediction Structure Probabilities Why Do We Assume Boltzmann We will give an argument from information theory. A. RNAfold预测RNA的二级结构 欢迎关注”生信修炼手册”! 在mirdeep软件的分析结果中，会提供miRNA前体的二级结构，这个结果实际上是通过调用 RNAfold 来实现的，该软件是一个经典的预测RNA二级结构的软件，网址如下SNP details*. The matched RNA loops are presented in both graphic and dot-bracket format. This algorithm is the second, and much larger, test case for ADPfusion. PDF. The filling colours of orange, green and blue indicate the base-pairing probability of below 0. The 3D template library of 3dRNA is constructed by decomposing RNA molecules with known 3D structures into SSEs. Compute Options will rerun RNAfold when you change their settings, so depending on the size of the sequence there may be a noticeable recompute time. Alan A. a RNAFold predictions of precursor RNA secondary structure in the context of designed spacers. Results The Vfold server offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b) three-dimensional structure from the two-dimensional structure and. The Fold server takes a sequence file of nucleic acids, either DNA or RNA, and folds it into its lowest free energy conformation. Vienna RNAfold from ViennaRNA package (version 2. , 2006). (B) An E-loop motif. If use SPOT-RNA-2D for your research, please cite the following papers:RNA molecules fold into complex structures that enable their diverse functions in cells. The old RNAalifold version where gaps are treated as characters. 0 we have enabled G-Quadruplex prediction support into RNAfold, RNAcofold, RNALfold, RNAalifold, RNAeval and RNAplot. 0 web server. 3, 0. had the minimal base pair. Quikfold. Vienna RNAfold是目前用户量最大的RNA结构分析平台，由奥地利维也纳大学开发。它使用热力学模型作为RNA结构预测模型，并采用自底向上的动态规划算法. the short sequence is hybridized to the best fitting part of the long one. Among them, we find folding of single and aligned sequences, prediction of RNA-RNA interactions, and design of sequences with a.