Results 61 to 70 of about 14,400 (274)

Multi-objective genetic algorithm for pseudoknotted RNA sequence design

Frontiers in Genetics, 2012
RNA inverse folding is a computational technology for designing RNA sequences which fold into a user-specified secondary structure. Although pseudoknots are functionally important motifs in RNA structures, less reports concerning the inverse folding of ...
Akito eTaneda
doaj   +1 more source

An RNA pseudoknot stimulates HTLV-1 pro-pol programmed −1 ribosomal frameshifting

RNA: A publication of the RNA Society, 2020
Programmed −1 ribosomal frameshifts (−1 PRFs) are commonly used by viruses to regulate their enzymatic and structural protein levels. Human T-cell leukemia virus type 1 (HTLV-1) is a carcinogenic retrovirus that uses two independent −1 PRFs to express ...
Eliza Thulson, Erik W. Hartwick, Andrew Cooper‐Sansone, M. A. C. Williams, Mary E Soliman, Leila K Robinson, J. Kieft, K. Mouzakis   +7 more
semanticscholar   +1 more source

Pseudoknots in RNA folding landscapes

Bioinformatics, 2015
Abstract Motivation: The function of an RNA molecule is not only linked to its native structure, which is usually taken to be the ground state of its folding landscape, but also in many cases crucially depends on the details of the folding pathways such as stable folding intermediates or the timing of the folding process itself. To model
Kucharik, Marcel, Hofacker, Ivo L., Stadler, Peter, Qin, Jing   +3 more
openaire   +4 more sources

Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions [PDF]

PLOS Computational Biology, 14(6): e1006222, 2018, 2019
RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological functions. Therefore, to predict 3D structures and stability of RNA pseudoknots is essential for understanding their functions.
arxiv   +1 more source

On the combinatorics of sparsification [PDF]

, 2012
Background: We study the sparsification of dynamic programming folding algorithms of RNA structures. Sparsification applies to the mfe-folding of RNA structures and can lead to a significant reduction of time complexity.
Christian M Reidys, Christian M Reidys, Fenix Wd Huang   +2 more
core   +6 more sources

McGenus: A Monte Carlo algorithm to predict RNA secondary structures with pseudoknots [PDF]

, 2012
We present McGenus, an algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus.
Andronescu, Bellaousov, Bon, Bon, Cristian Micheletti, Elliot, Hajiaghayi, Henri Orland, Lyngso, Markham, Mathews, McCaskill, Metzler, Michaël Bon, Nussinov, Orland, Orlandini, Reidys, Ren, Rivas, Tinoco, Vernizzi, Vernizzi, Wuchty, Xu, Zuker, Zwieb   +26 more
core   +3 more sources

DMfold: A Novel Method to Predict RNA Secondary Structure With Pseudoknots Based on Deep Learning and Improved Base Pair Maximization Principle

Frontiers in Genetics, 2019
While predicting the secondary structure of RNA is vital for researching its function, determining RNA secondary structure is challenging, especially for that with pseudoknots. Typically, several excellent computational methods can be utilized to predict
Linyu Wang, Linyu Wang, Yuanning Liu, Yuanning Liu, Xiaodan Zhong, Xiaodan Zhong, Xiaodan Zhong, Haiming Liu, Haiming Liu, Chao Lu, Chao Lu, Cong Li, Cong Li, Hao Zhang, Hao Zhang   +14 more
doaj   +1 more source

Altering SARS Coronavirus Frameshift Efficiency Affects Genomic and Subgenomic RNA Production

Viruses, 2013
In previous studies, differences in the amount of genomic and subgenomic RNA produced by coronaviruses with mutations in the programmed ribosomal frameshift signal of ORF1a/b were observed.
Ewan P. Plant, Deborah R. Taylor, Jonathan D. Dinman, Ralph S. Baric, Amy C. Sims   +4 more
doaj   +1 more source

Graph-Theoretic Partitioning of RNAs and Classification of Pseudoknots-II [PDF]

arXiv, 2021
Dual graphs have been applied to model RNA secondary structures with pseudoknots, or intertwined base pairs. In previous works, a linear-time algorithm was introduced to partition dual graphs into maximally connected components called blocks and determine whether each block contains a pseudoknot or not.
arxiv  

The gene coding for small ribosomal subunit RNA in the basidiomycete Ustilago maydis contains a group I intron [PDF]

, 1992
The nucleotide sequence of the gene coding for small ribosomal subunit RNA in the basidiomycete Ustilago maydis was determined. It revealed the presence of a group I intron with a length of 411 nucleotides.
De Wachter, Rupert, Neefs, Jean-Marc, Goris, Anne, Van de Peer, Yves   +3 more
core   +1 more source