scholarly journals Memory efficient folding algorithms for circular RNA secondary structures

2006 ◽  
Vol 22 (10) ◽  
pp. 1172-1176 ◽  
Author(s):  
I. L. Hofacker ◽  
P. F. Stadler
Keyword(s):  
Secondary Structures ◽  
Circular Rna ◽  
Rna Secondary Structures ◽  
Memory Efficient

scholarly journals Mutually exclusive RNA secondary structures regulate translation initiation of DinQ in Escherichia coli

RNA ◽  
2016 ◽  
Vol 22 (11) ◽  
pp. 1739-1749 ◽  
Author(s):  
Knut I. Kristiansen ◽  
Ragnhild Weel-Sneve ◽  
James A. Booth ◽  
Magnar Bjørås
Keyword(s):  
Escherichia Coli ◽  
Translation Initiation ◽  
Secondary Structures ◽  
Rna Secondary Structures

Interval-Based Similarity for Classifying Conserved RNA Secondary Structures

2016 ◽  
Vol 31 (3) ◽  
pp. 78-85 ◽  
Author(s):  
Qingfeng Chen ◽  
Yi-Ping Phoebe Chen ◽  
Chengqi Zhang
Keyword(s):  
Secondary Structures ◽  
Rna Secondary Structures

scholarly journals Integration of Expressed Sequence Tag Data Flanking Predicted RNA Secondary Structures Facilitates Novel Non-Coding RNA Discovery

PLoS ONE ◽  
2011 ◽  
Vol 6 (6) ◽  
pp. e20561 ◽  
Author(s):  
Paul M. Krzyzanowski ◽  
Feodor D. Price ◽  
Enrique M. Muro ◽  
Michael A. Rudnicki ◽  
Miguel A. Andrade-Navarro
Keyword(s):  
Expressed Sequence Tag ◽  
Secondary Structures ◽  
Rna Secondary Structures ◽  
Non Coding Rna ◽  
Expressed Sequence

scholarly journals Protein-coding structured RNAs: A computational survey of conserved RNA secondary structures overlapping coding regions in drosophilids

Biochimie ◽  
2011 ◽  
Vol 93 (11) ◽  
pp. 2019-2023 ◽  
Author(s):  
Sven Findeiß ◽  
Jan Engelhardt ◽  
Sonja J. Prohaska ◽  
Peter F. Stadler
Keyword(s):  
Secondary Structures ◽  
Protein Coding ◽  
Rna Secondary Structures ◽  
Coding Regions

Large-scale Investigation of Long Noncoding RNA Secondary Structures in Human and Mouse

2018 ◽  
Vol 13 (5) ◽  
pp. 450-460 ◽  
Author(s):  
Xingli Guo ◽  
Lin Gao ◽  
Yu Wang ◽  
David K.Y. Chiu ◽  
Bingbo Wang ◽  
...  
Keyword(s):  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Large Scale ◽  
Secondary Structures ◽  
Rna Secondary Structures ◽  
Human And Mouse

scholarly journals DCJ-RNA - double cut and join for RNA secondary structures

2017 ◽  
Vol 18 (S12) ◽  
Author(s):  
Ghada H. Badr ◽  
Haifa A. Al-aqel
Keyword(s):  
Secondary Structures ◽  
Rna Secondary Structures ◽  
Double Cut And Join

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.

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