Results 41 to 50 of about 9,562,225 (293)

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, Evans, DJ; id_orcid   +6 more
core   +1 more source

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

, 2019
The majority of our human genome transcribes into noncoding RNAs with unknown structures and functions. Obtaining functional clues for noncoding RNAs requires accurate base-pairing or secondary-structure prediction.
Zhou, Yaoqi, Hanson, Jack, Paliwal, Kuldip, Singh, Jaswinder   +3 more
core   +1 more source

A novel end-to-end method to predict RNA secondary structure profile based on bidirectional LSTM and residual neural network

BMC Bioinformatics, 2021
Background Studies have shown that RNA secondary structure, a planar structure formed by paired bases, plays diverse vital roles in fundamental life activities and complex diseases.
Linyu Wang, Xiaodan Zhong, Shuo Wang, Hao Zhang, Yuanning Liu   +4 more
doaj   +1 more source

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures.: [PDF]

, 2015
This paper is a report of a second round of RNA-Puzzles, a collective and blind experiment in three-dimensional (3D) RNA structure prediction. Three puzzles, Puzzles 5, 6, and 10, represented sequences of three large RNA structures with limited or no ...
Serganov, A. (A), Dunin-Horkawicz, S. (S), Masquida, B. (Benoit), Westhof, E. (Eric), Purzycka, K. (K) J. (J), Xu, X. (X), Cruz, J. (J) A. (A), Blanchet, M. (M) F. (F), Adamiak, R. (R) W. (W), Cordero, P. (P), Kladwang, W. (W), Matelska, D. (D), Meyer, M. (Melanie), Chojnowski, G. (G), Wang, J. (J), Boniecki, M. (M), Stasiewicz, J. (J), Miao, Z. (Zhichao), Szachniuk, M. (M), Zhang, J. (J), Dokholyan, N. (N) V. (V), Zhao, P. (P), Tandon, A. (A), Chou, F. (F) C. (C), Major, F. (F), Zok, T. (T), Cheng, C. (C), Tian, S. (S), Chen, S. (S) J. (J), Mann, T. (T) H. (H), Lach, G. (G), Magnus, M. (M), Popenda, M. (M), Xiao, Y. (Y), Das, R. (R), Krokhotin, A. (A), Bujnicki, J. (J) M. (M), Peselis, A. (A), Ferré-D'amaré, A. (A) R. (R), Ding, F. (F), Chou, Fang-Chieh, Blanchet, Marc-Frédérick, Zhao, Peinan, Łach, Grzegorz, Matelska, Dorota, Major, François, Purzycka, Katarzyna J., Ding, Feng, Szachniuk, Marta, Miao, Zhichao, Peselis, Alla, Chen, Shi-Jie, Kladwang, Wipapat, Xiao, Yi, Adamiak, Ryszard W., Popenda, Mariusz, Serganov, Alexander, Masquida, Benoît, Meyer, Melanie, Zok, Tomasz, Xu, Xiaojun, Bujnicki, Janusz M., Almeida Cruz, Jose, Das, Rhiju, Boniecki, Michał, Stasiewicz, Juliusz, Mann, Thomas, H., Ferré-D’amaré, Adrian, R, Wang, Jian, Magnus, Marcin, Chojnowski, Grzegorz, Tian, Siqi, Krokhotin, Andrey, Westhof, Eric, Dokholyan, Nikolay, V, Tandon, Arpit, Dunin-Horkawicz, Stanisław, Cheng, Clarence, Cordero, Pablo, Zhang, Jinwei   +79 more
core   +1 more source

RNA structure prediction: Progress and perspective [PDF]

Chinese Physics B, 2014
23 ...
Shi, Ya-Zhou, Wu, Yuan-Yan, Wang, Feng-Hua, Tan, Zhi-Jie   +3 more
openaire   +2 more sources

Novel endoribonucleases as central players in various pathways of eukaryotic RNA metabolism [PDF]

, 2010
For a long time it has been assumed that the decay of RNA in eukaryotes is mainly carried out by exoribonucleases, which is in contrast to bacteria, where endoribonucleases are well documented to initiate RNA degradation.
Tomecki, Rafał, Dziembowski, Andrzej
core   +3 more sources

Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction

BMC Bioinformatics, 2004
Background RNA secondary structure prediction methods based on probabilistic modeling can be developed using stochastic context-free grammars (SCFGs).
Eddy Sean R, Dowell Robin D
doaj   +1 more source

Evolutionary Algorithm for RNA Secondary Structure Prediction Based on Simulated SHAPE Data. [PDF]

PLoS ONE, 2016
Non-coding RNAs perform a wide range of functions inside the living cells that are related to their structures. Several algorithms have been proposed to predict RNA secondary structure based on minimum free energy.
Soheila Montaseri, Mohammad Ganjtabesh, Fatemeh Zare-Mirakabad   +2 more
doaj   +1 more source

Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics [PDF]

, 2004
Reeder J, Giegerich R. Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics. 2004;5(1): 104.Background: The general problem of RNA secondary structure prediction under the widely ...
Reeder Jens, Jens Reeder, Robert Giegerich, Reeder, Jens, Giegerich, Robert, Giegerich Robert   +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
doaj   +1 more source