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Sparsification of RNA structure prediction including pseudoknots

Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, S Cenk Sahinalp
2010 Algorithms for Molecular Biology  
Although sparsification has been applied to a number of RNA-related structure prediction problems in the past few years, we provide the first application of sparsification to pseudoknotted RNA structure  ...  Although many RNA molecules contain pseudoknots, computational prediction of pseudoknotted RNA structure is still in its infancy due to high running time and space consumption implied by the dynamic programming  ...  Contributions We study sparsification of pseudoknotted RNA structure prediction.  ... 
doi:10.1186/1748-7188-5-39 pmid:21194463 pmcid:PMC3161351 fatcat:f2tmuqj3snej5o4g76vnocrpia

Sparsification of RNA Structure Prediction Including Pseudoknots [chapter]

Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, S. Cenk Sahinalp
2010 Lecture Notes in Computer Science  
Although sparsification has been applied to a number of RNA-related structure prediction problems in the past few years, we provide the first application of sparsification to pseudoknotted RNA structure  ...  Although many RNA molecules contain pseudoknots, computational prediction of pseudoknotted RNA structure is still in its infancy due to high running time and space consumption implied by the dynamic programming  ...  Contributions We study sparsification of pseudoknotted RNA structure prediction.  ... 
doi:10.1007/978-3-642-15294-8_4 fatcat:53ezg7r4vjbw7dhs5xpu4ytrlq

On the combinatorics of sparsification

Fenix WD Huang, Christian M Reidys
2012 Algorithms for Molecular Biology  
The sparsification of the Λ * -decomposition rule for RNA pseudoknotted structures of genus 1 leads to an expected number of candidates of Θ(n 2 ).  ...  Results: We analyze the sparsification of a particular decomposition rule, Λ * , that splits an interval for RNA secondary and pseudoknot structures of fixed topological genus.  ...  We want to thank an anonymous referee for pointing out an incorrect assumption of first version of this paper. His comments have led to a much improved version of the paper. 23  ... 
doi:10.1186/1748-7188-7-28 pmid:23088372 pmcid:PMC3549849 fatcat:clgsxls75nfmre65mkjownizwe

Sparse RNA folding revisited: space-efficient minimum free energy structure prediction

Sebastian Will, Hosna Jabbari
2016 Algorithms for Molecular Biology  
RNA secondary structure prediction by energy minimization is the central computational tool for the analysis of structural non-coding RNAs and their interactions.  ...  Sparsification has been successfully applied to improve the time efficiency of various structure prediction algorithms while guaranteeing the same result; however, for many such folding problems, space  ...  Acknowledgements We thank Anne Condon for fruitful discussions about RNA pseudoknot prediction.  ... 
doi:10.1186/s13015-016-0071-y pmid:27110275 pmcid:PMC4842305 fatcat:mki73to3e5cjbfyyi2zyzmx57e

On the combinatorics of sparsification [article]

Fenix W. D. Huang, Christian M. Reidys
2012 arXiv   pre-print
Results: We analyze the sparsification of a particular decomposition rule, Λ^*, that splits an interval for RNA secondary and pseudoknot structures of fixed topological genus.  ...  We study the sparsification of dynamic programming folding algorithms of RNA structures.  ...  We want to thank an anonymous referee for pointing out an incorrect assumption of first version of this paper. His comments have led to a much improved version of the paper.  ... 
arXiv:1201.0308v2 fatcat:ztfysip5ezb7ppatiivrrhp5ca

Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding [chapter]

Raheleh Salari, Mathias Möhl, Sebastian Will, S. Cenk Sahinalp, Rolf Backofen
2010 Lecture Notes in Computer Science  
In this paper we show how to reduce both the time and space complexity of RNA-RNA interaction prediction problem as described by Alkan et al. [1] by a linear factor via dynamic programming sparsification  ...  By the use of polymer-zeta property for RNA-structures, we demonstrate that ψ(n) = O(n) on average.  ...  The sparsification of these cases works in close analogy to the sparsification of RNA structure prediction as described by Wexler et al. [32] .  ... 
doi:10.1007/978-3-642-12683-3_31 fatcat:c4wd7k5n7ba2nkulfzotcdftca

Knotify: An Efficient Parallel Platform for RNA Pseudoknot Prediction Using Syntactic Pattern Recognition

Christos Andrikos, Evangelos Makris, Angelos Kolaitis, Georgios Rassias, Christos Pavlatos, Panayiotis Tsanakas
2022 Methods and Protocols  
Having focused on the pseudoknot predictions, we formalized the secondary structure prediction of the RNA to be primarily a parsing and, secondly, an optimization problem.  ...  Capturing these clues relies on accurate "base pairing" prediction, also known as "RNA secondary structure prediction".  ...  In [78] , the proposed deep-learning framework DMfold predicts the secondary structure of RNA sequences, including pseudoknots.  ... 
doi:10.3390/mps5010014 pmid:35200530 pmcid:PMC8876629 fatcat:ao2zvmqlrfc2dkhbljheqyweoa

PRACTICALITY AND TIME COMPLEXITY OF A SPARSIFIED RNA FOLDING ALGORITHM

SLAVICA DIMITRIEVA, PHILIPP BUCHER
2012 Journal of Bioinformatics and Computational Biology  
Commonly used RNA folding programs compute the minimum free energy structure of a sequence under the pseudoknot exclusion constraint. They are based on Zuker's algorithm which runs in time Oðn 3 Þ.  ...  Recently, it has been claimed that RNA folding can be achieved in average time Oðn 2 Þ using a sparsification technique.  ...  Recently sparsification was also applied to algorithms for prediction of pseudoknotted RNA structures. 13 In this work, we introduce another version of sparsification for RNA folding algorithms and perform  ... 
doi:10.1142/s0219720012410077 pmid:22809342 fatcat:vpicei3fbnahbg5sts67rixsmi

An Efficient Algorithm for Upper Bound on the Partition Function of Nucleic Acids

Hamidreza Chitsaz, Elmirasadat Forouzmand, Gholamreza Haffari
2013 Journal of Computational Biology  
Even structure prediction by sampling from the ensemble and clustering those structures by Sfold [7] has proven to be more reliable than minimum free energy structure prediction.  ...  It has been shown that minimum free energy structure for RNAs and RNA-RNA interaction is often incorrect due to inaccuracies in the energy parameters and inherent limitations of the energy model.  ...  In the absence of high throughput experimental assays to observe RNA structure and RNA-RNA interactions, the problems of RNA structure prediction and RNA-RNA interaction prediction gain the highest priority  ... 
doi:10.1089/cmb.2013.0003 pmid:23829650 fatcat:emvrvcrkirckbkflbrr3dpreay

An Efficient Algorithm for Upper Bound on the Partition Function of Nucleic Acids [article]

Hamidreza Chitsaz and Elmirasadat Forouzmand and Gholamreza Haffari
2013 arXiv   pre-print
Even structure prediction by sampling from the ensemble and clustering those structures by Sfold [7] has proven to be more reliable than minimum free energy structure prediction.  ...  It has been shown that minimum free energy structure for RNAs and RNA-RNA interaction is often incorrect due to inaccuracies in the energy parameters and inherent limitations of the energy model.  ...  In the absence of high throughput experimental assays to observe RNA structure and RNA-RNA interactions, the problems of RNA structure prediction and RNA-RNA interaction prediction gain the highest priority  ... 
arXiv:1301.1590v1 fatcat:qc6rdylds5fv7lkvbw7r5dqymi

A max-margin training of RNA secondary structure prediction integrated with the thermodynamic model [article]

Manato Akiyama, Kengo Sato, Yasubumi Sakakibara
2017 bioRxiv   pre-print
Motivation: A popular approach for predicting RNA secondary structure is the thermodynamic nearest neighbor model that finds a thermodynamically most stable secondary structure with the minimum free energy  ...  Results: In this paper, we propose a novel algorithm for RNA secondary structure prediction that integrates the thermodynamic approach and the machine learning based weighted approach.  ...  Conflict of Interest: none declared.  ... 
doi:10.1101/205047 fatcat:bqwnbtvskjcw5fds43gvcnidrm

Consistent Consideration of RNA Structural Alignments Improves Prediction Accuracy of RNA Secondary Structures [article]

Masaki Tagashira
2020 bioRxiv   pre-print
The probabilistic consideration of the global pairwise sequence alignment of two RNAs tied with their global single secondary structures, or global pairwise structural alignment, is known to predict more  ...  ConsHomfold and ConsAlifold, which predict the global single and consensus secondary structures of unaligned and aligned homologs considering consistently preferable (or sparse) global pairwise structural  ...  Most computations were performed on the NIG supercomputer at the ROIS National Institute of Genetics.  ... 
doi:10.1101/2020.07.14.199893 fatcat:irb27po4wbgojfdiwzfnf65cwa

A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms [chapter]

Yann Ponty, Cédric Saule
2011 Lecture Notes in Computer Science  
SauleHypergraph RNA Folding Including Pseudoknots Yann Ponty, Cédric SauleHypergraph RNA Folding Including Pseudoknots 11 / 22  ...  Extensions: Predicting interactions, RNA design, Simultaneous folding and alignment Thanks to Yann Ponty, Cédric Saule Hypergraph RNA Folding Including Pseudoknots 19 / 22 Yann Ponty, Cédric  ... 
doi:10.1007/978-3-642-23038-7_22 fatcat:ilfxsopinnd7zhhiswsztyuzpm

Freiburg RNA tools: a central online resource for RNA-focused research and teaching

Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu (+10 others)
2018 Nucleic Acids Research  
Open education resources offer interactive visualizations of RNA structure and RNA-RNA interaction prediction as well as basic and advanced sequence alignment algorithms.  ...  The webserver includes RNA-RNA interaction prediction (IntaRNA, CopraRNA, metaMIR), sRNA homology search (GLASSgo), sequence-structure alignments (LocARNA, MARNA, CARNA, ExpaRNA), CRISPR repeat classification  ...  ACKNOWLEDGEMENTS We thank the users of the Freiburg RNA tools for their productive feedback. FUNDING  ... 
doi:10.1093/nar/gky329 pmid:29788132 pmcid:PMC6030932 fatcat:cmpvl5tygrc27mbc5qyjv7pzaq

Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions

Stefan E Seemann, Andreas S Richter, Jan Gorodkin, Rolf Backofen
2010 Algorithms for Molecular Biology  
One of the advantages of our approach (in contrast to other RNA-RNA interaction prediction methods) is the application of covariance detection and prediction of pseudoknots between intra-and inter-molecular  ...  Predicting these RNA interactions is essential for functional studies of putative ncRNAs or for the design of artificial RNAs.  ...  Acknowledgements We thank Bjarne Knudsen for inspiring discussions about extensions of the Pfold method.  ... 
doi:10.1186/1748-7188-5-22 pmid:20492641 pmcid:PMC2903599 fatcat:jcqjghofgbctjcktpy3nbar5bm
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