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A Linear Inside-Outside Algorithm for Correcting Sequencing Errors in Structured RNAs
[chapter]
2013
Lecture Notes in Computer Science
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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
2013
Journal of Computational Biology
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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]
2013
arXiv
pre-print
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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
2011
BMC Bioinformatics
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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
2012
BMC Bioinformatics
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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
2015
BMC Bioinformatics
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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
2009
PLoS Computational Biology
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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
2005
Bioinformatics
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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
2018
International Journal of Biological Sciences
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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]
2020
arXiv
pre-print
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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
2016
BMC Bioinformatics
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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
2006
Bioinformatics
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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
2005
Journal of Bioinformatics and Computational Biology
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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]
2019
bioRxiv
pre-print
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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
2010
Physical Review E
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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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