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CENTROIDFOLD: a web server for RNA secondary structure prediction

K. Sato, M. Hamada, K. Asai, T. Mituyama
2009 Nucleic Acids Research  
The CENTROIDFOLD web server (http://www.ncrna.org/ centroidfold/) is a web application for RNA secondary structure prediction powered by one of the most accurate prediction engine.  ...  For a multiple alignment sequence, the server predicts a common secondary structure. Usage of the server is quite simple.  ...  ACKNOWLEDGEMENTS We thank Hisanori Kiryu and our colleagues from the RNA Informatics Team at the Computational Biology Research Center (CBRC) for fruitful discussions. Conflict of interest statement.  ... 
doi:10.1093/nar/gkp367 pmid:19435882 pmcid:PMC2703931 fatcat:qefdivlltnhddhelh3g3ft6kz4

Rtools: a web server for various secondary structural analyses on single RNA sequences

Michiaki Hamada, Yukiteru Ono, Hisanori Kiryu, Kengo Sato, Yuki Kato, Tsukasa Fukunaga, Ryota Mori, Kiyoshi Asai
2016 Nucleic Acids Research  
We implemented a web server of the tools to predict secondary structures and to calculate various structural features based on the energy models of secondary structures.  ...  According to the thermodynamic model, however, the probability of any secondary structure is very small. As a consequence, any tool to predict the secondary structures of RNAs has limited accuracy.  ...  CentroidFold CentroidFold (8) predicts a pseudo-knot-free RNA secondary structure from an individual RNA sequence.  ... 
doi:10.1093/nar/gkw337 pmid:27131356 pmcid:PMC4987903 fatcat:44xyphwf4raf7p6jfxtu6jngh4

Artificial Intelligence in Aptamer–Target Binding Prediction

Zihao Chen, Long Hu, Bao-Ting Zhang, Aiping Lu, Yaofeng Wang, Yuanyuan Yu, Ge Zhang
2021 International Journal of Molecular Sciences  
We also performed analysis to compare the accuracy of different secondary and tertiary structure prediction methods for aptamers.  ...  For this part, we review the secondary and tertiary structure prediction methods for aptamers, molecular docking, as well as molecular dynamic simulation methods for aptamer–target binding.  ...  In the previous study, the CentroidFold web server was used to predict the secondary structures of RNA aptamers targeting angiopoietin-2 [29] .  ... 
doi:10.3390/ijms22073605 pmid:33808496 fatcat:efmv3lbfkbhktopagqdtutkkem

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

T. Puton, L. P. Kozlowski, K. M. Rother, J. M. Bujnicki
2014 Nucleic Acids Research  
Regrettably, PETfold pre2.0 did not validate the correct type of input data, and for unaligned data sets, it generated RNA secondary structure predictions, which scored poorly in our benchmark.  ...  We recalculated all predictions for PETfold pre2.0 with aligned RNA sequences (the same data sets as used for other methods that required aligned sequences).  ...  Ext TurboFold(seed) (W: 52, L: 1, NW: 0) Table 4 . 4 Data sets used for benchmarking methods predicting RNA secondary structure Source Data set name Type of RNAs Sequence length Number of  ... 
doi:10.1093/nar/gku208 pmid:24682823 pmcid:PMC4005657 fatcat:panuadtpqvaa5lq6hx6erke3mm

Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming

Y. Kato, K. Sato, K. Asai, T. Akutsu
2012 Nucleic Acids Research  
We present a web-based tool set Rtips 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 with pseudoknots and RactIP for predicting RNA-RNA interactions with kissing hairpins  ...  ACKNOWLEDGEMENTS The authors would like to thank all people who are involved in discussion about improvement on the server and testing the robustness.  ... 
doi:10.1093/nar/gks412 pmid:22600734 pmcid:PMC3394313 fatcat:yfg7rgc2zzee5a4b7aj42uj5qe

CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs

Haruka Yonemoto, Kiyoshi Asai, Michiaki Hamada
2013 International Journal of Molecular Sciences  
In this paper, we describe a fast and accurate web server, called CentroidAlign-Web, which can handle long RNA sequences.  ...  The web server also appropriately incorporates information about known secondary structures into MSAs.  ...  Acknowledgments This work was supported in part by MEXT KAKENHI (Grant-in-Aid for Young Scientists (A):  ... 
doi:10.3390/ijms14036144 pmid:23507751 pmcid:PMC3634467 fatcat:me7y2czkija7hl4ctfqdnaaztq

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

Tomasz Puton, Lukasz P. Kozlowski, Kristian M. Rother, Janusz M. Bujnicki
2013 Nucleic Acids Research  
We present a continuous benchmarking approach for the assessment of RNA secondary structure prediction methods implemented in the CompaRNA web server.  ...  Benchmarks on both data sets offer insight into the relative performance of RNA secondary structure prediction methods on RNAs of different size and with respect to different types of structure.  ...  ACKNOWLEDGEMENTS The authors thank the developers of RNA structure prediction methods analyzed in this work for making them freely available.  ... 
doi:10.1093/nar/gkt101 pmid:23435231 pmcid:PMC3627593 fatcat:46y43oiui5bb3kobe6rakzgqgq

Development of a Functionally Minimized Mutant of the R3C Ligase Ribozyme Offers Insight into the Plausibility of the RNA World Hypothesis

Eri Kurihara, Sayuri Uchida, Takuya Umehara, Koji Tamura
2014 Biology  
The three-way junction structure was necessary to maintain enzymatic function and the stability of the "grip" (P4 + P5) stem had a large influence on the catalytic activity of R3C.  ...  The final minimized ribozyme we obtained comprised ~50 nucleotides, comparable to the estimated length of prebiotically synthesized RNA.  ...  ), and the program for the development of strategic research center in private universities by MEXT, Japan.  ... 
doi:10.3390/biology3030452 pmid:25256424 pmcid:PMC4192621 fatcat:crpu3mcgorgqniwfak2hhoknri

RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning

Jaswinder Singh, Jack Hanson, Kuldip Paliwal, Yaoqi Zhou
2019 Nature Communications  
Obtaining functional clues for noncoding RNAs requires accurate base-pairing or secondary-structure prediction.  ...  The proposed method (SPOT-RNA), with a freely available server and standalone software, should be useful for improving RNA structure modeling, sequence alignment, and functional annotations.  ...  The web server provides an arc diagram and a 2D diagram of predicted RNA secondary structure through Visualization Applet for RNA (VARNA) 69 Acknowledgements This work was supported by Australia  ... 
doi:10.1038/s41467-019-13395-9 pmid:31776342 pmcid:PMC6881452 fatcat:sppjpfdvxffjlfcoqhofirb5be

Ensemble-based prediction of RNA secondary structures

Nima Aghaeepour, Holger H Hoos
2013 BMC Bioinformatics  
evaluation of existing RNA secondary structure prediction procedures.  ...  Accurate structure prediction methods play an important role for the understanding of RNA function.  ...  Acknowledgements We thank Anne Condon and Mirela Andronescu for their insightful comments on this work, and Dave Brent for help with setting up the web server for the AveRNA software.  ... 
doi:10.1186/1471-2105-14-139 pmid:23617269 pmcid:PMC3750279 fatcat:7qg76twdpzarhkfvo6tkckjxcy

Fighting against uncertainty: An essential issue in bioinformatics [article]

Michiaki Hamada
2013 arXiv   pre-print
Many bioinformatics problems, such as sequence alignment, gene prediction, phylogenetic tree estimation and RNA secondary structure prediction, are often affected by the "uncertainty" of a solution; that  ...  The methods include (i) avoiding point estimation, (ii) maximum expected accuracy (MEA) estimations, and (iii) several strategies to design a pipeline involving several prediction methods.  ...  Acknowledgement This work was supported in part by MEXT KAKENHI (Grant-in-Aid for Young Scientists (A): 24680031). I am grateful to Dr. Martin Frith, Dr. Dave duVerle and Prof.  ... 
arXiv:1305.3655v1 fatcat:w6z54dcdubaghmv3lsfqcncw2e

Prediction of RNA secondary structure by maximizing pseudo-expected accuracy

Michiaki Hamada, Kengo Sato, Kiyoshi Asai
2010 BMC Bioinformatics  
Recent studies have revealed the importance of considering the entire distribution of possible secondary structures in RNA secondary structure predictions; therefore, a new type of estimator is proposed  ...  Conclusions: This study gives not only a method for predicting the secondary structure that balances between sensitivity and PPV, but also a general method for approximately maximizing the (pseudo-)expected  ...  Sato K, Hamada M, Asai K, Mituyama T: CENTROID- FOLD: a web server for RNA secondary structure prediction. Nucleic Acids Res. 2009, 37:W277-280. 33.  ... 
doi:10.1186/1471-2105-11-586 pmid:21118522 pmcid:PMC3003279 fatcat:s75xuh5ndjhgxo5buymwgsyhou

Design of RNAs: comparing programs for inverse RNA folding

Alexander Churkin, Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl, Danny Barash
2017 Briefings in Bioinformatics  
Given a secondary structure, these programs aim to predict sequences that fold into a target minimum free energy secondary structure, while considering various constraints.  ...  It is geared for specific tasks requiring RNA design based on input secondary structure, with an outlook toward the future of RNA design programs.  ...  JW is supported by a NSERC Discovery Grant (Rgpin 386596-10) and NSERC Accelerator Supplement (Rgpas 477873-15).  ... 
doi:10.1093/bib/bbw120 pmid:28049135 pmcid:PMC6018860 fatcat:nnyqx4rv6ndyfpoztbahh46exu

UFold: Fast and Accurate RNA Secondary Structure Prediction with Deep Learning [article]

Yingxin Cao, Laiyi Fu, Jie Wu, Qing Nie, Xiaohui Xie
2020 bioRxiv   pre-print
For many RNA molecules, the secondary structure is essential for the correction function of the RNA.  ...  Predicting RNA secondary structure from nucleotide sequences is a long-standing problem in genomics, but the prediction performance has reached a plateau over time.  ...  Funding This work was partially supported by NSF IIS-1715017, NSF DMS-1763272, NIH U54-CA217378, and a Simons Foundation grant (594598). Conflict of Interest: None declared.  ... 
doi:10.1101/2020.08.17.254896 fatcat:gpd5c43cxvbv7norkgkygrwm6e

Kinetic Study of the Avocado Sunblotch Viroid Self-Cleavage Reaction Reveals Compensatory Effects between High-Pressure and High-Temperature: Implications for Origins of Life on Earth

Hussein Kaddour, Honorine Lucchi, Guy Hervé, Jacques Vergne, Marie-Christine Maurel
2021 Biology  
The behavior of ASBVd results from the involvement of the hammerhead ribozyme present at its catalytic domain, indeed a structural motif is very widespread in the ancient and current RNA world.  ...  These results provide information about the structural aspects or this self-cleavage reaction, which is involved in the process of maturation of this viroid.  ...  Together with Pierre Douzou, Gaston pioneered the use of high pressures and low temperatures in studying structure-function relationships in biomacromolecules.  ... 
doi:10.3390/biology10080720 fatcat:mou7hob2djfqnimxjqfwho6zfq
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