Results 31 to 40 of about 526,558 (303)

The Rainbow Spectrum of RNA Secondary Structures [PDF]

Bulletin of Mathematical Biology, 2018
In this paper we analyze the length-spectrum of rainbows in RNA secondary structures. A rainbow in a secondary structure is a maximal arc with respect to the partial order induced by nesting. We show that there is a significant gap in this length-spectrum.
Li, Thomas J. X., Reidys, Christian M.
openaire   +4 more sources

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, Yili Wang, Yuanning Liu, Yuanning Liu, Shuo Wang, Shuo Wang, Zhen Liu, Zhen Liu, Zhen Liu, Yubing Gao, Yubing Gao, Hao Zhang, Hao Zhang, Liyan Dong, Liyan Dong   +14 more
doaj   +1 more source

Detection of genome-scale ordered RNA structure (GORS) in genomes of positive-stranded RNA viruses:Implications for virus evolution and host persistence [PDF]

, 2004
Discrete RNA secondary and higher-order structures, typically local in extent, play a fundamental role in RNA virus replication. Using new bioinformatics analysis methods, we have identified genome-scale ordered RNA structure (GORS) in many genera and ...
Evans, David J, Simmonds, Peter, Tuplin, Andrew, Tuplin, A, Evans, DJ, Simmonds, P   +5 more
core   +1 more source

Secondary structure prediction for RNA sequences including N6-methyladenosine

Nature Communications, 2022
RNA folding free energy nearest neighbor parameters were determined for sequences with the nucleotide m6A. The RNAstructure software package can accommodate modified nucleotides, enabling secondary structure prediction of sequences with m6A.
Elzbieta Kierzek, Xiaoju Zhang, Richard M. Watson, Scott D. Kennedy, Marta Szabat, Ryszard Kierzek, David H. Mathews   +6 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, Qingfeng Chen, Yongjie Li, Cheng Luo   +3 more
doaj   +1 more source

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

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, Yuhong Zhang, Guixing Zheng, Bingxia Chen, Mengxin Zhang, Jian Li, Tao Peng, Jun Huang, Xinhua Wang   +8 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, Giraud, Mathieu, de Monte, Antoine, Touzet, Hélène   +3 more
openaire   +4 more sources

A hepatitis C virus cis-acting replication element forms a long-range RNA-RNA interaction with upstream RNA sequences in NS5B [PDF]

, 2008
The genome of hepatitis C virus (HCV) contains cis-acting replication elements (CREs) comprised of RNA stem-loop structures located in both the 5' and 3' non-coding regions (NCR), and in the NS5B coding sequence.
Diviney, Sinéad, Elliot, R., Evans, David John, Evans, D., Armstrong, V, Tuplin, Andrew, Evans, D.J., Struthers, Madeleine, Struthers, M., Elliott, Richard M., Diviney, S., Tuplin, A., Armstrong, V., Struthers, M, Simmonds, Peter, Elliott, Richard Michael, Armstrong, Victoria, Tuplin, A, Evans, David J., Simmonds, P., Diviney, S, Elliott, R.M., Simmonds, P   +22 more
core   +1 more source

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, Xi Li, Min Dong, Mitchell Graham, Nehul Yadav, Chun Liang   +5 more
doaj   +1 more source

Combinatorics of RNA secondary structures

Discrete Applied Mathematics, 1998
zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Ivo L. Hofacker, Peter Schuster 0002, Peter F. Stadler   +2 more
openaire   +2 more sources