Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores
BMC Bioinformatics, 2015 RNA pseudoknots play important roles in many biological processes. Previous methods for comparative pseudoknot analysis mainly focus on simultaneous folding and alignment of RNA sequences.
Yang Song, Lei Hua, B. Shapiro, J. Wang
semanticscholar +1 more source
Pseudoknots: RNA Structures with Diverse Functions
PLoS Biology, 2005 Just as proteins form distinct structural motifs, certain structures are commonly adopted by RNA molecules. Amongst the most prevalent is the RNA pseudoknot.
David W. Staple, Samuel E. Butcher
openaire +5 more sources
Combinatorial Analysis for Pseudoknot RNA with Complex Structure [PDF]
arXiv, 2019 There exists many complicated $k$-noncrossing pseudoknot RNA structures in nature based on some special conditions. The special characteristic of RNA structures gives us great challenges in researching the enumeration, prediction and the analysis of prediction algorithm.
arxiv
Absolute quantification of translational regulation and burden using combined sequencing approaches
Molecular Systems Biology, 2019 Translation of mRNAs into proteins is a key cellular process. Ribosome binding sites and stop codons provide signals to initiate and terminate translation, while stable secondary mRNA structures can induce translational recoding events.
Thomas E Gorochowski +5 more
doaj +1 more source
RNA-LEGO: Combinatorial Design of Pseudoknot RNA [PDF]
arXiv, 2007 In this paper we enumerate $k$-noncrossing RNA pseudoknot structures with given minimum stack-length. We show that the numbers of $k$-noncrossing structures without isolated base pairs are significantly smaller than the number of all $k$-noncrossing structures.
arxiv
An NMR and Mutational Study of the Pseudoknot Within the Gene 32 mRNA of Bacteriophage T2: Insights into a Family of Structurally Related RNA Pseudoknots [PDF]
, 1997 Zhihua Du, David W. Hoffman
openalex +1 more source
A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes [PDF]
, 1999 Timothy S. Wadkins +4 more
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Inverse folding of RNA pseudoknot structures [PDF]
arXiv, 2009 Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These interactions are called pseudoknots and are observed across the whole spectrum of RNA functionalities.
arxiv
The role of the pseudoknot at the 3' end of turnip yellow mosaic virus RNA in minus-strand synthesis by the viral RNA-dependent RNA polymerase [PDF]
, 1997 Birgit Deiman +2 more
openalex +1 more source
A pseudoknot‐compatible universal site is located in the large ribosomal RNA in the peptidyltransferase center [PDF]
, 1999 V. I. Ivanov +5 more
openalex +1 more source