Results 31 to 40 of about 10,995,303 (306)

Mutations designed to modify the NS gene mRNA secondary structure affect influenza A pathogenicity in vivo [PDF]

, 2021
The influenza A virus genome consists of eight segments of negative-sense RNA that encode up to 18 proteins. During the process of viral replication, positive-sense (+)RNA (cRNA) or messenger RNA (mRNA) is synthesized.
A. S. Taraskin, A. V. Vasin, A. A. Lozhkov, I. L. Baranovskaya, M. V. Sergeeva   +4 more
core   +1 more source

A comprehensive comparison of comparative RNA structure prediction approaches [PDF]

, 2004
Gardner PP, Giegerich R. A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics. 2004;5(1): 140.Background: An increasing number of researchers have released novel RNA structure analysis and prediction ...
Giegerich, R., Gardner, Paul P., Gardner, P. P., Paul P Gardner, Robert Giegerich, Giegerich, Robert, Giegerich Robert, Gardner Paul P   +7 more
core   +1 more source

N6‐methyladenosine and RNA secondary structure affect transcript stability and protein abundance during systemic salt stress in Arabidopsis

Plant Direct, 2020
After transcription, a messenger RNA (mRNA) is further post‐transcriptionally regulated by several features including RNA secondary structure and covalent RNA modifications (specifically N6‐methyladenosine, m6A). Both RNA secondary structure and m6A have
Marianne C. Kramer, Kevin A. Janssen, Kyle Palos, Andrew D. L. Nelson, Lee E. Vandivier, Benjamin A. Garcia, Eric Lyons, Mark A. Beilstein, Brian D. Gregory   +8 more
doaj   +1 more source

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

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

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, Töller, Thomas, Giegerich, Robert, Kurtz, Stefan   +3 more
openaire   +4 more sources

RNAmute: RNA secondary structure mutation analysis tool

BMC Bioinformatics, 2006
Background RNAMute is an interactive Java application that calculates the secondary structure of all single point mutations, given an RNA sequence, and organizes them into categories according to their similarity with respect to the wild type predicted ...
Barash Danny, Churkin Alexander
doaj   +1 more source

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

The influence of viral RNA secondary structure on interactions with innate host cell defences [PDF]

, 2013
RNA viruses infecting vertebrates differ fundamentally in their ability to establish persistent infections with markedly different patterns of transmission, disease mechanisms and evolutionary relationships with their hosts.
Blundell, Richard, Richard Blundell, Nora McFadden, Joris J. Maarleveld, Maarleveld, Joris J, Evans, David J, Simmonds, Peter, Jeroen Witteveldt, Maarleveld, Joris J., David J. Evans, McFadden, Nora, Peter Simmonds, Evans, David J., Witteveldt, Jeroen, Evans, David J.; id_orcid   +14 more
core   +1 more source

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, Yang Liu, Xiaochun Hu, Patrick Wang, Xichun Li, Jun Wu   +5 more
doaj   +1 more source