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CENTROIDFOLD: a web server for RNA secondary structure prediction
2009
Nucleic Acids Research
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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
2016
Nucleic Acids Research
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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
2021
International Journal of Molecular Sciences
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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
2014
Nucleic Acids Research
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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
2012
Nucleic Acids Research
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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
2013
International Journal of Molecular Sciences
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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
2013
Nucleic Acids Research
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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
2014
Biology
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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
2019
Nature Communications
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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
2013
BMC Bioinformatics
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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]
2013
arXiv
pre-print
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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
2010
BMC Bioinformatics
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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
2017
Briefings in Bioinformatics
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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]
2020
bioRxiv
pre-print
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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
2021
Biology
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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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