Results 51 to 60 of about 14,834 (261)

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   +7 more sources

Shapes of RNA Pseudoknot Structures [PDF]

Journal of Computational Biology, 2010
24 pages, 7 figures,
Reidys, Christian M., Wang, Rita R.
openaire   +3 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   +4 more sources

Structural conservation in the template/pseudoknot domain of vertebrate telomerase RNA from teleost fish to human [PDF]

Proceedings of the National Academy of Sciences of the United States of America, 2016
Yaqiang Wang, Joseph D. Yesselman, Qi Zhang, Mijeong Kang, Juli Feigon   +4 more
openalex   +2 more sources

An RNA pseudoknot is essential for standby-mediated translation of the tisB toxin mRNA in Escherichia coli

Nucleic Acids Research, 2020
In response to DNA damage, Escherichia coli cells activate the expression of the toxin gene tisB of the toxin–antitoxin system tisB-istR1. Of three isoforms, only the processed, highly structured +42 tisB mRNA is active.
Cédric Romilly, Anne Lippegaus, E. Wagner   +2 more
semanticscholar   +1 more source

Pseudoknot-Generating Operation

Theoretical Computer Science, 2016
zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Cho, Da-Jung, Han, Yo-Sub, Ng, Timothy, Salomaa, Kai   +3 more
openaire   +2 more sources

TT2NE: A novel algorithm to predict RNA secondary structures with pseudoknots [PDF]

, 2010
We present TT2NE, a new algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus.
Bailor, Bellaousov, Bon, Dam, Dirks, Doshi, Elliot, Friedman, Henri Orland, Kuo, Lyngso, Mathews, McCaskill, Metzler, Michaël Bon, Nussinov, Orland, Pillsbury, Reeder, Ren, Rivas, Rivas, Ruan, Shen, t'Hooft, Tinoco, Vernizzi, Zhao, Zuker, Zuker   +29 more
core   +5 more sources

An O(n^5) algorithm for MFE prediction of kissing hairpins and 4-chains in nucleic acids [PDF]

, 2008
Efficient methods for prediction of minimum free energy (MFE) nucleic secondary structures are widely used, both to better understand structure and function of biological RNAs and to design novel nano-structures.
Chen, Ho-Lin, Condon, Anne, Jabbari, Hosna   +2 more
core   +3 more sources

The internal initiation of translation in bovine viral diarrhea virus RNA depends on the presence of an RNA pseudoknot upstream of the initiation codon

Virology Journal, 2007
Background Bovine viral diarrhea virus (BVDV) is the prototype representative of the pestivirus genus in the Flaviviridae family. It has been shown that the initiation of translation of BVDV RNA occurs by an internal ribosome entry mechanism mediated by ...
Moes Lorin, Wirth Manfred
doaj   +1 more source

TransUFold: Unlocking the structural complexity of short and long RNA with pseudoknots

Mathematical Biosciences and Engineering, 2023
The RNA secondary structure is like a blueprint that holds the key to unlocking the mysteries of RNA function and 3D structure. It serves as a crucial foundation for investigating the complex world of RNA, making it an indispensable component of research
Yunxiang Wang, Hong Zhang , Zhenchao Xu, Shouhua Zhang, Rui Guo   +4 more
doaj   +1 more source