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

BMC Bioinformatics ◽

10.1186/1471-2105-12-103 ◽

2011 ◽

Vol 12 (1) ◽

Author(s):

Zsuzsanna Sükösd ◽

Bjarne Knudsen ◽

Morten Værum ◽

Jørgen Kjems ◽

Ebbe S Andersen

Keyword(s):

Secondary Structure ◽

Structure Prediction ◽

Rna Secondary Structure ◽

Secondary Structure Prediction ◽

Rna Secondary Structure Prediction ◽

Stochastic Context Free Grammars ◽

Context Free ◽

Context Free Grammars

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RNA secondary structure prediction using stochastic context-free grammars and evolutionary history

Bioinformatics ◽

10.1093/bioinformatics/15.6.446 ◽

1999 ◽

Vol 15 (6) ◽

pp. 446-454 ◽

Author(s):

B. Knudsen ◽

J. Hein

Keyword(s):

Secondary Structure ◽

Structure Prediction ◽

Rna Secondary Structure ◽

Evolutionary History ◽

Secondary Structure Prediction ◽

Rna Secondary Structure Prediction ◽

Stochastic Context Free Grammars ◽

Context Free ◽

Context Free Grammars

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Applying Length-Dependent Stochastic Context-Free Grammars to RNA Secondary Structure Prediction

10.3390/a4040223 ◽

2011 ◽

Vol 4 (4) ◽

pp. 223-238 ◽

Author(s):

Frank Weinberg ◽

Markus E. Nebel

Keyword(s):

Secondary Structure ◽

Structure Prediction ◽

Rna Secondary Structure ◽

Secondary Structure Prediction ◽

Rna Secondary Structure Prediction ◽

Stochastic Context Free Grammars ◽

Context Free ◽

Context Free Grammars

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Parallel RNA secondary structure prediction using stochastic context-free grammars

Concurrency and Computation Practice and Experience ◽

10.1002/cpe.952 ◽

2005 ◽

Vol 17 (14) ◽

pp. 1669-1685 ◽

Author(s):

Tong Liu ◽

Bertil Schmidt

Keyword(s):

Secondary Structure ◽

Structure Prediction ◽

Rna Secondary Structure ◽

Secondary Structure Prediction ◽

Rna Secondary Structure Prediction ◽

Stochastic Context Free Grammars ◽

Context Free ◽

Context Free Grammars

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Evolving stochastic context--free grammars for RNA secondary structure prediction

BMC Bioinformatics ◽

10.1186/1471-2105-13-78 ◽

2012 ◽

Vol 13 (1) ◽

pp. 78 ◽

Author(s):

James WJ Anderson ◽

Paula Tataru ◽

Joe Staines ◽

Jotun Hein ◽

Rune Lyngsø

Keyword(s):

Secondary Structure ◽

Structure Prediction ◽

Rna Secondary Structure ◽

Secondary Structure Prediction ◽

Rna Secondary Structure Prediction ◽

Stochastic Context Free Grammars ◽

Context Free ◽

Context Free Grammars

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Pfold: RNA secondary structure prediction using stochastic context-free grammars

Nucleic Acids Research ◽

10.1093/nar/gkg614 ◽

2003 ◽

Vol 31 (13) ◽

pp. 3423-3428 ◽

Author(s):

Bjarne Knudsen ◽

Jotun Hein

Keyword(s):

Secondary Structure ◽

Structure Prediction ◽

Rna Secondary Structure ◽

Secondary Structure Prediction ◽

Rna Secondary Structure Prediction ◽

Stochastic Context Free Grammars ◽

Context Free ◽

Context Free Grammars

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Approximation and Exact Algorithms for RNA Secondary Structure Prediction and Recognition of Stochastic Context-Free Languages

Algorithms and Computation - Lecture Notes in Computer Science ◽

10.1007/3-540-49381-6_36 ◽

1998 ◽

pp. 338-347 ◽

Author(s):

Tatsuya Akutsu

Keyword(s):

Secondary Structure ◽

Structure Prediction ◽

Rna Secondary Structure ◽

Secondary Structure Prediction ◽

Exact Algorithms ◽

Rna Secondary Structure Prediction ◽

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Faculty Opinions recommendation of COFOLD: an RNA secondary structure prediction method that takes co-transcriptional folding into account.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718010599.793476797 ◽

2013 ◽

Author(s):

Scott Silverman

Keyword(s):

Secondary Structure ◽

Structure Prediction ◽

Rna Secondary Structure ◽

Secondary Structure Prediction ◽

Prediction Method ◽

Rna Secondary Structure Prediction ◽

Structure Prediction Method ◽

Secondary Structure Prediction Method

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A Discrete Hopfield Neural Network Based MIS Finding Algorithm for Stems Selecting and Its Application in RNA Secondary Structure Prediction

Chinese Journal of Computers ◽

10.3724/sp.j.1016.2008.00051 ◽

2009 ◽

Vol 31 (1) ◽

pp. 51-58

Author(s):

Qi LIU ◽

Yin ZHANG ◽

Xiu-Zi YE ◽

Rong-Dong YU

Keyword(s):

Neural Network ◽

Secondary Structure ◽

Structure Prediction ◽

Rna Secondary Structure ◽

Secondary Structure Prediction ◽

Hopfield Neural Network ◽

Rna Secondary Structure Prediction

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A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more

RNA ◽

10.1261/rna.030049.111 ◽

2011 ◽

Vol 18 (2) ◽

pp. 193-212 ◽

Author(s):

E. Rivas ◽

R. Lang ◽

S. R. Eddy

Keyword(s):

Secondary Structure ◽

Structure Prediction ◽

Rna Secondary Structure ◽

Probabilistic Models ◽

Nearest Neighbor ◽

Secondary Structure Prediction ◽

Rna Secondary Structure Prediction

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Evolutionary Algorithm for RNA Secondary Structure Prediction Based on Simulated SHAPE Data

PLoS ONE ◽

10.1371/journal.pone.0166965 ◽

2016 ◽

Vol 11 (11) ◽

pp. e0166965 ◽

Author(s):

Soheila Montaseri ◽

Mohammad Ganjtabesh ◽

Fatemeh Zare-Mirakabad

Keyword(s):

Secondary Structure ◽

Evolutionary Algorithm ◽

Structure Prediction ◽

Rna Secondary Structure ◽

Secondary Structure Prediction ◽

Rna Secondary Structure Prediction ◽

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