Results 31 to 40 of about 517,188 (256)
ATTfold: RNA Secondary Structure Prediction With Pseudoknots Based on Attention Mechanism
Frontiers in Genetics, 2020 Accurate RNA secondary structure information is the cornerstone of gene function research and RNA tertiary structure prediction. However, most traditional RNA secondary structure prediction algorithms are based on the dynamic programming (DP) algorithm ...
Yili Wang +14 more
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RNA Locally Optimal Secondary Structures [PDF]
Journal of Computational Biology, 2012 RNA locally optimal secondary structures provide a concise and exhaustive description of all possible secondary structures of a given RNA sequence, and hence a very good representation of the RNA folding space. In this paper, we present an efficient algorithm that computes all locally optimal secondary structures for any folding model that takes into ...
Saffarian, Azadeh +3 more
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Widespread selection for extremely high and low levels of secondary structure in coding sequences across all domains of life [PDF]
Open Biology, 2019 Codon composition, GC content and local RNA secondary structures can have a profound effect on gene expression, and mutations affecting these parameters, even though they do not alter the protein sequence, are not neutral in terms of selection.
Daniel Gebert +2 more
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Local similarity in RNA secondary structures [PDF]
Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003, 2004 We present a systematic treatment of alignment distance and local similarity algorithms on trees and forests. We build upon the tree alignment algorithm for ordered trees given by Jiang et. al (1995) and extend it to calculate local forest alignments, which is essential for finding local similar regions in RNA secondary structures.
Höchsmann, Matthias +3 more
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Graph-Based Analysis of RNA Secondary Structure Similarity Comparison
Complexity, 2021 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.
Lina Yang +5 more
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Classifying Conserved RNA Secondary Structures With Pseudoknots by Vector-Edit Distance
IEEE Access, 2021 Secondary structures have been proved to relate with the great functional diversity of RNA. There have been many studies to predict and compare the RNA secondary structures. However, fast and accurate comparison of RNA secondary structures with arbitrary
Liyu Huang +3 more
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Combinatorics of RNA secondary structures
Discrete Applied Mathematics, 1998 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Ivo L. Hofacker +2 more
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Frontiers in Cellular and Infection Microbiology, 2021 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
Yanwei Qi +8 more
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Review of machine learning methods for RNA secondary structure prediction.
PLoS Computational Biology, 2021 Secondary structure plays an important role in determining the function of noncoding RNAs. Hence, identifying RNA secondary structures is of great value to research. Computational prediction is a mainstream approach for predicting RNA secondary structure.
Qi Zhao +5 more
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JNSViewer-A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures. [PDF]
PLoS ONE, 2017 Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly
Jieming Shi +5 more
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