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A Linear Inside-Outside Algorithm for Correcting Sequencing Errors in Structured RNAs [chapter]

Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl
2013 Lecture Notes in Computer Science  
In this paper, we introduce RNApyro, an efficient linear-time and space inside-outside algorithm that computes exact mutational probabilities under secondary structure and evolutionary constraints given  ...  Analysis of the sequence-structure relationship in RNA molecules are essential to evolutionary studies but also to concrete applications such as error-correction methodologies in sequencing technologies  ...  In this model, the probability that the nucleotide at a given position needs to be mutated (i.e. corresponds to a sequencing error) can be computed using a variant of the Inside-Outside algorithm [4]  ... 
doi:10.1007/978-3-642-37195-0_17 fatcat:fboh3yx2djcm3hnxiwwqf7227u

Using Structural and Evolutionary Information to Detect and Correct Pyrosequencing Errors in Noncoding RNAs

Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl
2013 Journal of Computational Biology  
The analysis of the sequence-structure relationship in RNA molecules is not only essential for evolutionary studies but also for concrete applications such as error-correction in next generation sequencing  ...  In this article, we address the correction of NGS errors by calculating which mutations most increase the likelihood of a sequence to a given structure and RNA family.  ...  Acknowledgments The authors would like to thank Rob Knight for his suggestions and comments.  ... 
doi:10.1089/cmb.2013.0085 pmid:24134390 pmcid:PMC3822367 fatcat:yrxtgoil7fdqzh3fmasxa7szuu

Using structural and evolutionary information to detect and correct pyrosequencing errors in non-coding RNAs [article]

Vladimir Reinharz, Yann Ponty , Jérôme Waldispühl
2013 arXiv   pre-print
In this paper, we introduce RNApyro, an efficient linear-time and space inside-outside algorithm that computes exact mutational probabilities under secondary structure and evolutionary constraints given  ...  Analysis of the sequence-structure relationship in RNA molecules are essential to evolutionary studies but also to concrete applications such as error-correction methodologies in sequencing technologies  ...  Acknowledgments The authors would like to thank Rob Knight for his suggestions and comments.  ... 
arXiv:1305.7068v1 fatcat:hr6xeqwvvbbi5gxlq7suunngve

Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars

Zsuzsanna Sükösd, Bjarne Knudsen, Morten Værum, Jørgen Kjems, Ebbe S Andersen
2011 BMC Bioinformatics  
Results: We have distributed both the phylogenetic calculations and the inside-outside algorithm in PPfold, resulting in a significant reduction of runtime on multicore machines.  ...  The pfold model couples a stochastic context-free grammar to phylogenetic analysis for a high accuracy in predictions, but the time complexity of the algorithm and underflow errors have prevented its use  ...  This research has been funded by the Danish Agency for Science, Technology, and Innovation under the project "PC Mini-Grids for Prediction of Viral RNA Structure and Evolution", #09-061856.  ... 
doi:10.1186/1471-2105-12-103 pmid:21501497 pmcid:PMC3102635 fatcat:ov7nndlc3jcklgargjfs5m5bba

Evaluating the effect of disturbed ensemble distributions on SCFG based statistical sampling of RNA secondary structures

Anika Scheid, Markus E Nebel
2012 BMC Bioinformatics  
samples of the entire ensemble of feasible structures for a particular input sequence.  ...  Recently, a novel probabilistic method for the prediction of RNA secondary structures from a single sequence has been studied which is based on generating statistically representative and reproducible  ...  All authors wish to thank an anonymous reviewer for careful reading and helpful remarks and suggestions made for a previous version of this article.  ... 
doi:10.1186/1471-2105-13-159 pmid:22776037 pmcid:PMC3871765 fatcat:jxixc6iyqngovhlvxcnyakdxom

Algebraic Dynamic Programming over general data structures

Christian zu Siederdissen, Sonja J Prohaska, Peter F Stadler
2015 BMC Bioinformatics  
In addition to rephrasing the well-known algorithms for HMMs, pairwise sequence alignment, and RNA folding we show how the TSP and the shortest Hamiltonian path problem can be implemented efficiently in  ...  This allows us to formalize the conceptual complementarity of inside and outside variables in a natural way.  ...  Acknowledgements This work was funded, in part, by the Austrian FWF, project "SFB F43 RNA regulation of the transcriptome", the Templeton Foundation, grant # 24332 "Origins and Evolution of Regulation  ... 
doi:10.1186/1471-2105-16-s19-s2 pmid:26695390 pmcid:PMC4686793 fatcat:7m7ipfhy7vgwtfvkqjqoa32d3i

Evolutionary Triplet Models of Structured RNA

Robert K. Bradley, Ian Holmes, Gary D. Stormo
2009 PLoS Computational Biology  
We implemented the above algorithms for a simple model of pairwise RNA structural evolution; in particular, the algorithms for maximum likelihood (ML) alignment of three known RNA structures and a known  ...  We describe a "transducer composition" algorithm for extending pairwise probabilistic models of RNA structural evolution to models of multiple sequences related by a phylogenetic tree.  ...  Acknowledgments We thank Jeff Thorne, Jamie Cate, Jennifer Doudna, Jotun Hein, David Haussler, Sean Eddy, Elena Rivas and Eric Westhof for inspirational discussions.  ... 
doi:10.1371/journal.pcbi.1000483 pmid:19714212 pmcid:PMC2725318 fatcat:s4vau6jkhrgyfdjlrgda7u6phm

RNA secondary structural alignment with conditional random fields

K. Sato, Y. Sakakibara
2005 Bioinformatics  
Since comparative sequence analysis is effective for non-coding RNA detection, efficient computational methods are expected for structural alignment of RNA sequences.  ...  Results: We propose a novel approach for RNA structural alignment based on conditional random fields (CRFs).  ...  The expectation E s,t [F ] can be computed efficiently by using a variant of the inside-outside algorithm.  ... 
doi:10.1093/bioinformatics/bti1139 pmid:16204111 fatcat:uqzv54qb2rcmjl2l72gnbgiqsq

Research on folding diversity in statistical learning methods for RNA secondary structure prediction

Yu Zhu, ZhaoYang Xie, YiZhou Li, Min Zhu, Yi-Ping Phoebe Chen
2018 International Journal of Biological Sciences  
The existing prediction methods for a single sequence do not fully consider the folding diversity which may occur among RNAs with different functions or sources.  ...  How to improve the prediction accuracy of RNA secondary structure is currently a hot topic.  ...  The inside algorithm gives the probability that G (a grammar model) generates ω (an RNA sequence): The classification correct rate is usually used as the evaluation index.  ... 
doi:10.7150/ijbs.24595 pmid:29989089 pmcid:PMC6036747 fatcat:kzyc7yxkdjb7tgtvvg7h7h3opu

LinearPartition: Linear-Time Approximation of RNA Folding Partition Function and Base Pairing Probabilities [article]

He Zhang, Liang Zhang, David H. Mathews, Liang Huang
2020 arXiv   pre-print
Inspired by the success of our recently proposed LinearFold algorithm that predicts the approximate MFE structure in linear time, we design a similar linear-time heuristic algorithm, LinearPartition, to  ...  However, the classical partition function algorithm scales cubically with sequence length, and is therefore a slow calculation for long sequences.  ...  After the partition-function calculation, also known as the "inside" phase of the classical insideoutside algorithm 39 , we design a similar linear-time "outside" phase (see Supplementary Section A.3)  ... 
arXiv:1912.13190v3 fatcat:5mvrepm75ve6fev4wj5ea5r3he

Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome

Risa Kawaguchi, Hisanori Kiryu
2016 BMC Bioinformatics  
Conclusions: We have shown that ParasoR is very useful for analyzing the structural properties of long RNA sequences such as mRNAs, pre-mRNAs, and long non-coding RNAs whose lengths can be more than a  ...  In particular, we observed a highly significant preference for base pairing over entire intronic regions as compared to their antisense sequences, as well as to intergenic regions.  ...  Hofacker for the useful ViennaRNA package and Mirela Andronescu for providing us with innovative energy parameters for secondary structure prediction.  ... 
doi:10.1186/s12859-016-1067-9 pmid:27153986 pmcid:PMC4858847 fatcat:tdzvahqq5bbdnbwfhurcol7zqy

CONTRAfold: RNA secondary structure prediction without physics-based models

C. B. Do, D. A. Woods, S. Batzoglou
2006 Bioinformatics  
Motivation: For several decades, free energy minimization methods have been the dominant strategy for single sequence RNA secondary structure prediction.  ...  Results: In this paper, we present CONTRAfold, a novel secondary structure prediction method based on conditional log-linear models (CLLMs), a flexible class of probabilistic models which generalize upon  ...  Knudsen for assisting us with Pfold benchmarking, S. R. Eddy and A. Laederach for helpful comments, S. S. Gross and G. Asimenos for helpful discussions regarding algorithms and implementation, and A.  ... 
doi:10.1093/bioinformatics/btl246 pmid:16873527 fatcat:dgyvdrebejhqpo6ddprzwjpqsq

HIDDEN MARKOV MODELS, GRAMMARS, AND BIOLOGY: A TUTORIAL

SHIBAJI MUKHERJEE, SUSHMITA MITRA
2005 Journal of Bioinformatics and Computational Biology  
The basic algorithms and their application to analyzing biological sequences and modelling structures of bio-molecules like proteins and nucleic acids are discussed.  ...  Biological sequences and structures have been modelled using various machine learning techniques and abstract mathematical concepts.  ...  Inside outside The most popular algorithms for the estimation of the probabilities of a context free grammar are the Inside Outside algorithm and the Viterbi algorithm, both employing Maximum Likelihood  ... 
doi:10.1142/s0219720005001077 pmid:15852517 fatcat:elwanfaze5gejgvylj3p32zmmm

The mutational landscape of a prion-like domain [article]

Benedetta Bolognesi, Andre J. Faure, Mireia Seuma, Jörn M. Schmiedel, Gian Gaetano Tartaglia, Ben Lehner
2019 bioRxiv   pre-print
Our results demonstrate that deep mutagenesis is a powerful approach for probing the sequence-function relationships of intrinsically disordered proteins as well as their in vivo structural conformations  ...  For example, cytoplasmic aggregates of the RNA-binding protein TDP-43 are observed in 97% of cases of Amyotrophic Lateral Sclerosis (ALS)6,7.  ...  Acknowledgments and Funding Work in B.L.'s lab was supported by a European  ... 
doi:10.1101/592121 fatcat:35ckcvodbbb7vlgiypxu62tjhe

Three-dimensional structures of RNA obtained by means of knowledge-based interaction potentials

Oscar Taxilaga-Zetina, Patricia Pliego-Pastrana, Mauricio D. Carbajal-Tinoco
2010 Physical Review E  
Such interaction potentials are then used as the main constituents of a simplified simulation model, which is tested in the description of small secondary structure motifs.  ...  Our simulated RNA hairpins are consistent with the experimental structures obtained by NMR.  ...  Therefore, a classic problem of biophysics is the determination of the 3D native state of an RNA molecule, based on its linear sequence of nucleotides or primary structure.  ... 
doi:10.1103/physreve.81.041914 pmid:20481760 fatcat:w3y7kuk6dfaozli3woubh5uas4
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