Visualization of RNA secondary structure with pseudoknots

2021 ◽  
pp. 2150036
Author(s):  
Lina Yang ◽  
Yang Liu ◽  
Huiwu Luo ◽  
Xichun Li ◽  
Yuan Yan Tang
Keyword(s):  
Secondary Structure ◽  
Rna Secondary Structure ◽  
Large Scale ◽  
Secondary Structures ◽  
Combination Method ◽  
Joint Analysis ◽  
Discrete Wavelet ◽  
Visualization Method ◽  
Number Representation ◽  
Rna Secondary Structures

The function of pseudoknots cannot be ignored in the RNA secondary structure. Existing methods for analyzing RNA secondary structures with pseudoknots exhibit many shortcomings. This paper presents a novel RNA secondary structure visualization method in the case of a joint analysis of RNA primary structures and secondary structures. The way is based on the page number representation of the RNA secondary structure. It innovatively uses five vectors to represent bases, which are sequentially connected to outline the characteristics of the RNA secondary structure. The method covers almost all the constituent elements of the RNA secondary structure and extracts features completely. Experiments are based on the available techniques for large-scale annotation of RNA secondary structures, using a combination method of discrete wavelet transform and fractal dimension. The classification effect is compared with the previous RNA secondary structure representation methods. Experimental results show that the RNA secondary structure visualization method proposed in this paper has good application prospects in RNA secondary structure classification.

scholarly journals Graph-Based Analysis of RNA Secondary Structure Similarity Comparison

Complexity ◽  
2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Lina Yang ◽  
Yang Liu ◽  
Xiaochun Hu ◽  
Patrick Wang ◽  
Xichun Li ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Rna Secondary Structure ◽  
Noncoding Rna ◽  
Graphical Representation ◽  
Rna Virus ◽  
Distance Matrix ◽  
Secondary Structures ◽  
Discrete Wavelet ◽  
Rna Secondary Structures ◽  
Clustering Tree

In organisms, ribonucleic acid (RNA) plays an essential role. Its function is being discovered more and more. Due to the conserved nature of RNA sequences, its function mainly depends on the RNA secondary structure. The discovery of an approximate relationship between two RNA secondary structures helps to understand their functional relationship better. It is an important and urgent task to explore structural similarities from the graphical representation of RNA secondary structures. In this paper, a novel graphical analysis method based on the triple vector curve representation of RNA secondary structures is proposed. A combinational method involving a discrete wavelet transform (DWT) and fractal dimension with sliding window is introduced to analyze and compare the graphs derived from feature extraction; after that, the distance matrix is generated. Then, the distance matrix is analyzed by clustering and visualized as a clustering tree. RNA virus and noncoding RNA datasets are applied to perform experiments and analyze the clustering tree. The results show that the proposed method yields more accurate results in the comparison of RNA secondary structures.

scholarly journals RNA secondary structure prediction using deep learning with thermodynamic integration

2020 ◽  
Author(s):  
Kengo Sato ◽  
Manato Akiyama ◽  
Yasubumi Sakakibara
Keyword(s):  
Deep Learning ◽  
Secondary Structure ◽  
Structure Prediction ◽  
Rna Secondary Structure ◽  
Secondary Structure Prediction ◽  
Secondary Structures ◽  
Thermodynamic Integration ◽  
Rna Secondary Structure Prediction ◽  
Rna Secondary Structures ◽  
Non Coding Rnas

RNA secondary structure prediction is one of the key technologies for revealing the essential roles of functional non-coding RNAs. Although machine learning-based rich-parametrized models have achieved extremely high performance in terms of prediction accuracy, the risk of overfitting for such models has been reported. In this work, we propose a new algorithm for predicting RNA secondary structures that uses deep learning with thermodynamic integration, thereby enabling robust predictions. Similar to our previous work, the folding scores, which are computed by a deep neural network, are integrated with traditional thermodynamic parameters to enable robust predictions. We also propose thermodynamic regularization for training our model without overfitting it to the training data. Our algorithm (MXfold2) achieved the most robust and accurate predictions in computational experiments designed for newly discovered non-coding RNAs, with significant 2–10 % improvements over our previous algorithm (MXfold) and standard algorithms for predicting RNA secondary structures in terms of F-value.

scholarly journals Graphical Processing Unit - Supported RNA Secondary Structure Comparison

10.29007/bhsr ◽  
2020 ◽  
Author(s):  
Mutlu Mete ◽  
Abdullah Arslan
Keyword(s):  
Secondary Structure ◽  
Rna Secondary Structure ◽  
Secondary Structures ◽  
Graphical Processing Unit ◽  
Processing Unit ◽  
Structure Comparison ◽  
Rna Secondary Structures ◽  
Large Databases ◽  
Graphical Processing ◽  
Rna Secondary Structure Comparison

This study is part of our perpetual effort to develop improved RNA secondary structure analysis tools and databases. In this work we present a new Graphical Processing Unit (GPU)-based RNA structural analysis framework that supports fast multiple RNA secondary structure comparison for very large databases. A search-based secondary structure comparison algorithm deployed in RNASSAC website helps bioinformaticians find common RNA substructures from the underlying database. The algorithm performs two levels of binary searches on the database. Its time requirement is affected by the database size. Experiments on the RNASSAC website show that the algorithm takes seconds for a database of 4,666 RNAs. For example, it takes about 4.4 sec for comparing 25 RNAs from this database. In another case, when many non-overlapping common substructures are desired, a heuristic approach requires as long as 85 sec in comparing 40 RNAs from the same database. The comparisons by this sequential algorithm takes at least 50% more time when RNAs are compared from the database of several millions of RNAs. The most recently curated databases already have millions of RNA secondary structures. The improvement in run-time performance of comparison algorithms is necessary. This study present a GPU-based RNA substructure comparison algorithm with which running time for multiple RNA secondary structures remains feasible for large databases. Our new parallel algorithm is 12 times faster than the CPU version (sequential) comparison algorithm of the RNASSAC website. The response time significantly reduces towards development of a realtime RNA comparison web service for bioinformatics community.

A NON-PARAMETRIC BAYESIAN APPROACH FOR PREDICTING RNA SECONDARY STRUCTURES

2010 ◽  
Vol 08 (04) ◽  
pp. 727-742 ◽  
Author(s):  
KENGO SATO ◽  
MICHIAKI HAMADA ◽  
TOUTAI MITUYAMA ◽  
KIYOSHI ASAI ◽  
YASUBUMI SAKAKIBARA
Keyword(s):  
Secondary Structure ◽  
Bayesian Approach ◽  
Structure Prediction ◽  
Rna Secondary Structure ◽  
Secondary Structure Prediction ◽  
Secondary Structures ◽  
Generative Models ◽  
Rna Secondary Structures ◽  
Stochastic Context Free Grammars ◽  
Non Parametric

Since many functional RNAs form stable secondary structures which are related to their functions, RNA secondary structure prediction is a crucial problem in bioinformatics. We propose a novel model for generating RNA secondary structures based on a non-parametric Bayesian approach, called hierarchical Dirichlet processes for stochastic context-free grammars (HDP-SCFGs). Here non-parametric means that some meta-parameters, such as the number of non-terminal symbols and production rules, do not have to be fixed. Instead their distributions are inferred in order to be adapted (in the Bayesian sense) to the training sequences provided. The results of our RNA secondary structure predictions show that HDP-SCFGs are more accurate than the MFE-based and other generative models.

scholarly journals RNA secondary structure prediction using deep learning with thermodynamic integration

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Kengo Sato ◽  
Manato Akiyama ◽  
Yasubumi Sakakibara
Keyword(s):  
Free Energy ◽  
Deep Learning ◽  
Secondary Structure ◽  
Structure Prediction ◽  
Rna Secondary Structure ◽  
Nearest Neighbor ◽  
Secondary Structure Prediction ◽  
Secondary Structures ◽  
Rna Secondary Structures ◽  
Non Coding Rnas

AbstractAccurate predictions of RNA secondary structures can help uncover the roles of functional non-coding RNAs. Although machine learning-based models have achieved high performance in terms of prediction accuracy, overfitting is a common risk for such highly parameterized models. Here we show that overfitting can be minimized when RNA folding scores learnt using a deep neural network are integrated together with Turner’s nearest-neighbor free energy parameters. Training the model with thermodynamic regularization ensures that folding scores and the calculated free energy are as close as possible. In computational experiments designed for newly discovered non-coding RNAs, our algorithm (MXfold2) achieves the most robust and accurate predictions of RNA secondary structures without sacrificing computational efficiency compared to several other algorithms. The results suggest that integrating thermodynamic information could help improve the robustness of deep learning-based predictions of RNA secondary structure.

scholarly journals Detrended Fluctuation Analysis and Discrete Wavelet Transform for Similarity Comparison of RNA secondary structure

2020 ◽  
Author(s):  
Lina Yang ◽  
Yang Liu ◽  
Patrick Wang ◽  
Xichun Li
Keyword(s):  
Wavelet Transform ◽  
Secondary Structure ◽  
Detrended Fluctuation Analysis ◽  
Distance Matrix ◽  
Secondary Structures ◽  
Fluctuation Analysis ◽  
Discrete Wavelet ◽  
Rna Secondary Structures ◽  
Alignment Free ◽  
Detrended Fluctuation

Abstract Background Ribonucleic acid (RNA) is an important biological macromolecule. Through in-depth studies of RNA, its function has been increasingly discovered. The function of RNA is mostly dependent on its secondary structure because of its conserved nature. The discovery of an approximate relationship between two RNA secondary structures can help to understand their functional relationship better. This discovery can also help in exploring many unknown functions. Currently, RNA secondary structural similarity analysis methods are mainly divided into alignment-based methods and alignment-free methods. Alignment-free methods can obtain similarities and differences among RNA secondary structures more quickly and more accurately than alignment-based methods. Results In this paper, a novel alignment-free method based on the triple vector curve representation of RNA is proposed. A combinational method involving a discrete wavelet transform and detrended fluctuation analysis (DFA) with a sliding window is used to generate the distance matrix. Finally, a phylogenetic tree is constructed using the distance matrix. Experiments are performed on RNA viruses and non-coding RNA datasets, and the phylogenetic trees generated by different methods are compared. The results show that our method yields more accurate results in the comparison of RNA secondary structures. Conclusion The method in this paper enables a more accurate analysis of the similarities between RNA secondary structures. This method has certain application value in the comparison of RNA secondary structures, especially in the analysis of longer RNA sequences.

scholarly journals In Vivo and In Vitro Genome-Wide Profiling of RNA Secondary Structures Reveals Key Regulatory Features in Plasmodium falciparum

2021 ◽  
Vol 11 ◽  
Author(s):  
Yanwei Qi ◽  
Yuhong Zhang ◽  
Guixing Zheng ◽  
Bingxia Chen ◽  
Mengxin Zhang ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Rna Structure ◽  
Rna Secondary Structure ◽  
Secondary Structures ◽  
Rna Structures ◽  
Trophozoite Stage ◽  
Rna Secondary Structures ◽  
Biological Programme

It is widely accepted that the structure of RNA plays important roles in a number of biological processes, such as polyadenylation, splicing, and catalytic functions. Dynamic changes in RNA structure are able to regulate the gene expression programme and can be used as a highly specific and subtle mechanism for governing cellular processes. However, the nature of most RNA secondary structures in Plasmodium falciparum has not been determined. To investigate the genome-wide RNA secondary structural features at single-nucleotide resolution in P. falciparum, we applied a novel high-throughput method utilizing the chemical modification of RNA structures to characterize these structures. Structural data from parasites are in close agreement with the known 18S ribosomal RNA secondary structures of P. falciparum and can help to predict the in vivo RNA secondary structure of a total of 3,396 transcripts in the ring-stage and trophozoite-stage developmental cycles. By parallel analysis of RNA structures in vivo and in vitro during the Plasmodium parasite ring-stage and trophozoite-stage intraerythrocytic developmental cycles, we identified some key regulatory features. Recent studies have established that the RNA structure is a ubiquitous and fundamental regulator of gene expression. Our study indicate that there is a critical connection between RNA secondary structure and mRNA abundance during the complex biological programme of P. falciparum. This work presents a useful framework and important results, which may facilitate further research investigating the interactions between RNA secondary structure and the complex biological programme in P. falciparum. The RNA secondary structure characterized in this study has potential applications and important implications regarding the identification of RNA structural elements, which are important for parasite infection and elucidating host-parasite interactions and parasites in the environment.

scholarly journals Comparative analysis of coronavirus genomic RNA structure reveals conservation in SARS-like coronaviruses

2020 ◽  
Author(s):  
Wes Sanders ◽  
Ethan J. Fritch ◽  
Emily A. Madden ◽  
Rachel L. Graham ◽  
Heather A. Vincent ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Rna Structure ◽  
Rna Secondary Structure ◽  
Molecular Mechanisms ◽  
Selective Pressure ◽  
Secondary Structures ◽  
Rna Structures ◽  
Rna Secondary Structures ◽  
The Past ◽  
Novel Strategy

AbstractCoronaviruses, including SARS-CoV-2 the etiological agent of COVID-19 disease, have caused multiple epidemic and pandemic outbreaks in the past 20 years1–3. With no vaccines, and only recently developed antiviral therapeutics, we are ill equipped to handle coronavirus outbreaks4. A better understanding of the molecular mechanisms that regulate coronavirus replication and pathogenesis is needed to guide the development of new antiviral therapeutics and vaccines. RNA secondary structures play critical roles in multiple aspects of coronavirus replication, but the extent and conservation of RNA secondary structure across coronavirus genomes is unknown5. Here, we define highly structured RNA regions throughout the MERS-CoV, SARS-CoV, and SARS-CoV-2 genomes. We find that highly stable RNA structures are pervasive throughout coronavirus genomes, and are conserved between the SARS-like CoV. Our data suggests that selective pressure helps preserve RNA secondary structure in coronavirus genomes, suggesting that these structures may play important roles in virus replication and pathogenesis. Thus, disruption of conserved RNA secondary structures could be a novel strategy for the generation of attenuated SARS-CoV-2 vaccines for use against the current COVID-19 pandemic.

scholarly journals Using SHAPE-MaP To Model RNA Secondary Structure and Identify 3′UTR Variation in Chikungunya Virus

2020 ◽  
Vol 94 (24) ◽  
Author(s):  
Emily A. Madden ◽  
Kenneth S. Plante ◽  
Clayton R. Morrison ◽  
Katrina M. Kutchko ◽  
Wes Sanders ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Virus Replication ◽  
Rna Structure ◽  
Rna Secondary Structure ◽  
Chikungunya Virus ◽  
Secondary Structures ◽  
Rna Structures ◽  
Functional Importance ◽  
Rna Secondary Structures ◽  
Mosquito Cells

ABSTRACT Chikungunya virus (CHIKV) is a mosquito-borne alphavirus associated with debilitating arthralgia in humans. RNA secondary structure in the viral genome plays an important role in the lifecycle of alphaviruses; however, the specific role of RNA structure in regulating CHIKV replication is poorly understood. Our previous studies found little conservation in RNA secondary structure between alphaviruses, and this structural divergence creates unique functional structures in specific alphavirus genomes. Therefore, to understand the impact of RNA structure on CHIKV biology, we used SHAPE-MaP to inform the modeling of RNA secondary structure throughout the genome of a CHIKV isolate from the 2013 Caribbean outbreak. We then analyzed regions of the genome with high levels of structural specificity to identify potentially functional RNA secondary structures and identified 23 regions within the CHIKV genome with higher than average structural stability, including four previously identified, functionally important CHIKV RNA structures. We also analyzed the RNA flexibility and secondary structures of multiple 3′UTR variants of CHIKV that are known to affect virus replication in mosquito cells. This analysis found several novel RNA structures within these 3′UTR variants. A duplication in the 3′UTR that enhances viral replication in mosquito cells led to an overall increase in the amount of unstructured RNA in the 3′UTR. This analysis demonstrates that the CHIKV genome contains a number of unique, specific RNA secondary structures and provides a strategy for testing these secondary structures for functional importance in CHIKV replication and pathogenesis. IMPORTANCE Chikungunya virus (CHIKV) is a mosquito-borne RNA virus that causes febrile illness and debilitating arthralgia in humans. CHIKV causes explosive outbreaks but there are no approved therapies to treat or prevent CHIKV infection. The CHIKV genome contains functional RNA secondary structures that are essential for proper virus replication. Since RNA secondary structures have only been defined for a small portion of the CHIKV genome, we used a chemical probing method to define the RNA secondary structures of CHIKV genomic RNA. We identified 23 highly specific structured regions of the genome, and confirmed the functional importance of one structure using mutagenesis. Furthermore, we defined the RNA secondary structure of three CHIKV 3′UTR variants that differ in their ability to replicate in mosquito cells. Our study highlights the complexity of the CHIKV genome and describes new systems for designing compensatory mutations to test the functional relevance of viral RNA secondary structures.

scholarly journals bpRNA: Large-scale Automated Annotation and Analysis of RNA Secondary Structure

2018 ◽  
Author(s):  
Padideh Danaee ◽  
Mason Rouches ◽  
Michelle Wiley ◽  
Dezhong Deng ◽  
Liang Huang ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Single Molecule ◽  
Structure Prediction ◽  
Rna Secondary Structure ◽  
Large Scale ◽  
Secondary Structure Prediction ◽  
Sequence Data ◽  
Secondary Structures ◽  
Base Pairs ◽  
Statistical Trends

ABSTRACTWhile RNA secondary structure prediction from sequence data has made remarkable progress, there is a need for improved strategies for annotating the features of RNA secondary structures. Here we present bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with the positions, sequence, and flanking base pairs of each such structural feature. We also introduce several new informative representations of RNA structure types to improve structure visualization and interpretation. We have further used bpRNA to generate a web-accessible meta-database, “bpRNA-1m”, of over 100,000 single-molecule, known secondary structures; this is both more fully and accurately annotated and over 20-times larger than existing databases. We use a subset of the database with highly similar (≥90% identical) sequences filtered out to report on statistical trends in sequence, flanking base pairs, and length. Both the bpRNA method and the bpRNA-1m database will be valuable resources both for specific analysis of individual RNA molecules and large-scale analyses such as are useful for updating RNA energy parameters for computational thermodynamic predictions, improving machine learning models for structure prediction, and for benchmarking structure-prediction algorithms.

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