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Combinatorics of locally optimal RNA secondary structures [article]

Éric Fusy, Peter Clote
2012 arXiv   pre-print
Motivated by the kinetics of RNA secondary structure formation, we are interested in determining the asymptotic number of secondary structures that are locally optimal, with respect to a particular energy  ...  Locally optimal structures with respect to the base stacking energy model are exactly those secondary structures, whose stems cannot be extended.  ...  Enumeration of locally optimal secondary structures 4.1. Duality: RNA secondary structure ↔ weighted plane tree.  ... 
arXiv:1112.4610v3 fatcat:pjcdikjj7bh35lipi776kbcvaq

RNA Locally Optimal Secondary Structures

Azadeh Saffarian, Mathieu Giraud, Antoine de Monte, Hélène Touzet
2012 Journal of Computational Biology  
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  ...  In this paper, we present an efficient algorithm which computes all locally optimal secondary structures for any folding model that takes into account the stability of helical regions.  ...  This work shows that all locally optimal secondary structures of a given RNA can effectively be computed.  ... 
doi:10.1089/cmb.2010.0178 pmid:23057822 fatcat:gmz56f7rvrc55kyhg45dwaq5ue

Finding stable local optimal RNA secondary structures

Yuan Li, Shaojie Zhang
2011 Computer applications in the biosciences : CABIOS  
local optimal structures.  ...  By considering a reduced conformational space of local optimal stack configurations instead of all feasible RNA structures, we first present an algorithm for enumerating all possible local optimal stack  ...  In contrast, we are only interested in stable local optimal (SLOpt) structures.  ... 
doi:10.1093/bioinformatics/btr510 pmid:21903624 fatcat:tjhof5gsrrdwtbm4gycb5iqdwu

Combinatorics of locally optimal RNA secondary structures

Éric Fusy, Peter Clote
2012 Journal of Mathematical Biology  
Motivated by the kinetics of RNA secondary structure formation, we are interested in determining the asymptotic number of secondary structures that are locally optimal, with respect to a particular energy  ...  Locally optimal structures with respect to the base stacking energy model are exactly those secondary structures, whose stems cannot be extended.  ...  Enumeration of locally optimal secondary structures 4.1. Duality: RNA secondary structure ↔ weighted plane tree.  ... 
doi:10.1007/s00285-012-0631-9 pmid:23263300 fatcat:o5qcktpp6rhk3hi3ajbin2yxfu

RNALOSS: a web server for RNA locally optimal secondary structures

P. Clote
2005 Nucleic Acids Research  
The tool RNALOSS may be useful in designing RNA sequences which not only have low folding energy, but whose distribution of locally optimal secondary structures would suggest rapid and robust folding.  ...  We describe the web server RNALOSS, which provides information about the distribution of locally optimal secondary structures, that possibly form kinetic traps in the folding process.  ...  there appear to be fewer k-locally optimal secondary structures than in random RNA.  ... 
doi:10.1093/nar/gki382 pmid:15980545 pmcid:PMC1160143 fatcat:w2as7b7kujci3pvqulnu4asruq

RCPred: RNA complex prediction as a constrained maximum weight clique problem

Audrey Legendre, Eric Angel, Fariza Tahi
2019 BMC Bioinformatics  
We propose an original approach that takes advantage of the high number of RNA secondary structure and RNA-RNA interaction prediction tools.  ...  We formulate the problem of RNA complex prediction as the determination of the best combination (according to the free energy) of predicted RNA secondary structures and RNA-RNA interactions.  ...  RCPred is also able to provide sub-optimal solutions. Generating sub-optimal solutions is very important in RNA secondary structure prediction for several reasons.  ... 
doi:10.1186/s12859-019-2648-1 fatcat:satxqdi5drbi3kqgxlbuo26224

Stability of RNA stem-loop structure and distribution of non-random structure in the human immunodeficiency virus (HIV-I)

Shu-Yun Le, Jih-H Chen, Michael J. Braun, Matthew A. Gonda, Jacob V. Maizel
1988 Nucleic Acids Research  
The locally optimal secondary structure occurring in the 5' terminal region has been assessed using different overlapping segment sizes and the Monte Carlo method.  ...  The stability of potential RNA stem-loop structures in human immunodeficiency virus isolates, HTLV-III and ARV, has been calculated, and the relevance to the local significant secondary structures in the  ...  of the local optimal secondary structure in HTLV-III or ARV mRNA.  ... 
doi:10.1093/nar/16.11.5153 pmid:3387221 pmcid:PMC336724 fatcat:dxbudqeh7ffwbfttlne6hudaja

Computing the Partition Function for Kinetically Trapped RNA Secondary Structures

William A. Lorenz, Peter Clote, Cynthia Gibas
2011 PLoS ONE  
Here, we present a novel, efficient algorithm to compute the partition function over all locally optimal secondary structures of a given RNA sequence.  ...  An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely  ...  A preliminary report of this method was described in the poster paper Q34, ''Calculating Local Optima in the Turner Energy Model for RNA Secondary Structure'', presented by W.A. Lorenz and P.  ... 
doi:10.1371/journal.pone.0016178 pmid:21297972 pmcid:PMC3030561 fatcat:tcjavsf2wvcqxnbqxy6x3zisrq

RNALL: AN EFFICIENT ALGORITHM FOR PREDICTING RNA LOCAL SECONDARY STRUCTURAL LANDSCAPE IN GENOMES

XIU-FENG WAN, GUOHUI LIN, DONG XU
2006 Journal of Bioinformatics and Computational Biology  
The information of RNA local secondary structures (LSSs) can help retrieve biologically important motifs and study functions of RNA molecules.  ...  Most of the current RNA secondary structure prediction tools are not suitable for RNA LSS prediction on the genome scale due to high computational complexity.  ...  Background RNA local secondary structures (LSSs) can act as RNA structural motifs, which may function in various biological processes.  ... 
doi:10.1142/s0219720006002363 pmid:17099939 fatcat:demdenxbq5fahp5tm2vtstue2y

A Flexible Stem-Based Local Search Algorithm for Predicting RNA Secondary Structures Including Pseudoknots

Xiang Chen, Si-Min He, Dong-Bo Bu, Run-Sheng Chen, Wen Gao
2007 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering  
We demonstrate a new algorithm named FlexStem to predict RNA secondary structures with pseudoknots.  ...  By using a "maximal stem" and "stem merging" strategy, the search space for RNA structure prediction is significantly reduced.  ...  Although local search algorithms provide no guarantee on the optimality of a solution, we argue that it is still suitable for predicting RNA secondary structures with pseudoknots for a couple of reasons  ... 
doi:10.1109/bibe.2007.4375595 dblp:conf/bibe/ChenHBCG07 fatcat:6qu3b6svjzarrfpgpsfhxwb2du

RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data

Jason Yao, Vladimir Reinharz, François Major, Jérôme Waldispühl
2017 Nucleic Acids Research  
We recently developed a computational framework, named RNA-MoIP, to reconcile RNA secondary structure and local 3D motif information available in databases.  ...  RNA structures are hierarchically organized. The secondary structure is articulated around sophisticated local three-dimensional (3D) motifs shaping the full 3D architecture of the molecule.  ...  Between different RNAs, they are expected to share a similar local 3D structure based on folding interactions at the primary and secondary structure level.  ... 
doi:10.1093/nar/gkx575 pmid:28666332 pmcid:PMC5570209 fatcat:i7377ogjavdtzmul3geau7ytc4

RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data

Jason Yao, Vladimir Reinharz, François Major, Jérôme Waldispühl
2017 Nucleic Acids Research  
We recently developed a computational framework, named RNA-MoIP, to reconcile RNA secondary structure and local 3D motif information available in databases.  ...  RNA structures are hierarchically organized. The secondary structure is articulated around sophisticated local three-dimensional (3D) motifs shaping the full 3D architecture of the molecule.  ...  Between different RNAs, they are expected to share a similar local 3D structure based on folding interactions at the primary and secondary structure level.  ... 
doi:10.1093/nar/gkx429 pmid:28525607 pmcid:PMC5793723 fatcat:eschpy7oeng6jdtsr5a5kb43m4

RNA molecules with structure dependent functions are uniquely folded

S.-Y. Le
2002 Nucleic Acids Research  
Cis-acting elements in post-transcriptional regulation of gene expression are often correlated with distinct local RNA secondary structure.  ...  In this study, we introduce a computing method to calculate two quantitative measures, NRd and Stscr, for estimating the uniqueness of an RNA secondary structure.  ...  The program rna_match for structural comparisons can be accessed through the Internet at http://www. csd.uwo.ca/faculty/kzhang/rna/rna_match.html.  ... 
doi:10.1093/nar/gkf473 pmid:12177299 pmcid:PMC134240 fatcat:ae3t4f6qnfaddepdh3qzccztvy

A Hybrid Genetic Algorithm for RNA Structural Alignment

Abdesslem Layeb, Imen Bensetira, Kenza Bouaroudj
2011 International Journal of Computer Applications  
The RNA structural alignment is one of the most challenging tasks in bioinformatics. However, finding the accurate conserved structure of a set of RNA sequences is still being a difficult task.  ...  General Terms Algorithms,bioinformatic, metaheuristic, optimization problem.  ...  The secondary structure with the minimum free energy (MFE) has been regarded as the most reliable prediction of RNA secondary structures [14] .  ... 
doi:10.5120/2370-3120 fatcat:bfzdj5uf45gprlr6qf232dkymy

RNA Secondary Structures with Limited Base Pair Span: Exact Backtracking and an Application

Ronny Lorenz, Peter F. Stadler
2020 Genes  
The accuracy of RNA secondary structure prediction decreases with the span of a base pair, i.e., the number of nucleotides that it encloses.  ...  Here, we report on an efficient backtracking algorithm that reconstructs the globally optimal structure from the locally optimal fragments that are produced by the interleaved backtracking implemented  ...  Abbreviations The following abbreviations are used in this manuscript: MFE Minimum free energy (secondary structure) miRNA microRNA ncRNA Non-coding RNA MEA Maximum expected accuracy (secondary structure  ... 
doi:10.3390/genes12010014 pmid:33374382 fatcat:4b6cma4lxreifhuwta3tc4at44
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