Results 61 to 70 of about 14,834 (261)

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

Tolerance of Senecavirus A to Mutations in Its Kissing-Loop or Pseudoknot Structure Computationally Predicted in 3′ Untranslated Region

Frontiers in Microbiology, 2022
Senecavirus A (SVA) is an emerging virus that belongs to the genus Senecavirus in the family Picornaviridae. Its genome is a positive-sense and single-stranded RNA, containing two untranslated regions (UTRs).
Fuxiao Liu, Di Zhao, Di Zhao, Ning Wang, Ziwei Li, Ziwei Li, Yaqin Dong, Shuang Liu, Feng Zhang, Jin Cui, Hailan Meng, Bo Ni, Rong Wei, Hu Shan   +13 more
doaj   +1 more source

Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements. [PDF]

, 2017
In single stranded (+)-sense RNA viruses, RNA structural elements (SEs) play essential roles in the infection process from replication to encapsidation.
Aviran, Sharon, Choudhary, Krishna, Lucks, Julius B, Perry, Keith L, Thompson, Jeremy R, Watters, Kyle E   +5 more
core   +2 more sources

Combinatorics of RNA Structures with Pseudoknots [PDF]

Bulletin of Mathematical Biology, 2007
In this paper we derive the generating function of RNA structures with pseudoknots. We enumerate all $k$-noncrossing RNA pseudoknot structures categorized by their maximal sets of mutually intersecting arcs. In addition we enumerate pseudoknot structures over circular RNA. For 3-noncrossing RNA structures and RNA secondary structures we present a novel
Jin, Emma Y., Qin, Jing, Reidys, Christian M.   +2 more
openaire   +8 more sources

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, Goris, Anne, Neefs, Jean-Marc, Van de Peer, Yves   +3 more
core   +1 more source

Structural Alignment of Pseudoknotted RNA [PDF]

Journal of Computational Biology, 2006
In this paper, we address the problem of discovering novel non-coding RNA (ncRNA) using primary sequence, and secondary structure conservation, focusing on ncRNA families with pseudoknotted structures. Our main technical result is an efficient algorithm for computing an optimum structural alignment of an RNA sequence against a genomic substring.
Han, Buhm, Dost, Banu, Bafna, Vineet, Zhang, Shaojie   +3 more
openaire   +4 more sources

Psybrackets, pseudoknots and singular knots

Journal of Knot Theory and Its Ramifications, 2023
We introduce algebraic structures known as psybrackets and use them to define invariants of pseudoknots and singular knots and links. Psybrackets are Niebrzydowski tribrackets with additional structure inspired by the Reidemeister moves for pseudoknots and singular knots. Examples and computations are provided.
Jeong, Suhyeon, Kim, Jieon, Nelson, Sam
openaire   +2 more sources

Pseudoknot Formation Seeds the Twister Ribozyme Cleavage Reaction Coordinate

Journal of the American Chemical Society, 2017
Nikola Vušurović, Russ B. Altman, Daniel S. Terry, Ronald Micura, Scott C. Blanchard   +4 more
openalex   +2 more sources

RNA pseudoknots: folding and finding [PDF]

F1000 Biology Reports, 2010
RNA pseudoknots are important for function. Three-dimensional structural information is available, insights into factors affecting pseudoknot stability are being reported, and computer programs are available for predicting pseudoknots.
Liu, Biao, Mathews, David H, Turner, Douglas H   +2 more
openaire   +2 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