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pro vyhledávání: '"Zsuzsanna Sükösd"'
Publikováno v:
Methods in molecular biology (Clifton, N.J.). 1097
Stochastic context-free grammars (SCFGs) were first established in the context of natural language modelling, and only later found their applications in RNA secondary structure prediction. In this chapter, we discuss the basic SCFG algorithms (CYK an
Publikováno v:
Methods in Molecular Biology ISBN: 9781627037082
Stochastic context-free grammars (SCFGs) were first established in the context of natural language modelling, and only later found their applications in RNA secondary structure prediction. In this chapter, we discuss the basic SCFG algorithms (CYK an
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::a5c8feb03e805d166d0f411b397472d5
https://doi.org/10.1007/978-1-62703-709-9_8
https://doi.org/10.1007/978-1-62703-709-9_8
Publikováno v:
Sükösd, Z, Swenson, M S, Kjems, J & Heitsch, C E 2013, ' Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions ', Nucleic Acids Research, vol. 41, no. 5, pp. 2807-2816 . https://doi.org/10.1093/nar/gks1283
Nucleic Acids Research
Nucleic Acids Research
Recent advances in RNA structure determination include using data from high-throughput probing experiments to improve thermodynamic prediction accuracy. We evaluate the extent and nature of improvements in data-directed predictions for a diverse set
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ac8d65a78e47a6910aa95a61ca172fef
https://pure.au.dk/portal/da/publications/evaluating-the-accuracy-of-shapedirected-rna-secondary-structure-predictions(15458842-63fb-4871-8646-e2ca54bf17f6).html
https://pure.au.dk/portal/da/publications/evaluating-the-accuracy-of-shapedirected-rna-secondary-structure-predictions(15458842-63fb-4871-8646-e2ca54bf17f6).html
Autor:
James W. J. Anderson, Bjarne Knudsen, Zsuzsanna Sükösd, Christian N. S. Pedersen, Jørgen Kjems, Adam M. Novak
Publikováno v:
Sükösd, Z, Knudsen, B, Anderson, J WJ, Novák, A, Kjems, J & Pedersen, C N S 2013, ' Characterising RNA secondary structure space using information entropy ', B M C Bioinformatics, vol. 14, no. Suppl 2, S22, pp. 1-9 . https://doi.org/10.1186/1471-2105-14-S2-S22
BMC Bioinformatics
Scopus-Elsevier
BMC Bioinformatics
Scopus-Elsevier
Comparative methods for RNA secondary structure prediction use evolutionary information from RNA alignments to increase prediction accuracy. The model is often described in terms of stochastic context-free grammars (SCFGs), which generate a probabili
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https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0d28db8b8e6efea34e12154d38a1b00e
https://pure.au.dk/portal/da/publications/characterising-rna-secondary-structure-space-using-information-entropy(2d736e45-c4f5-4682-bc7a-f5b8ab1a4262).html
https://pure.au.dk/portal/da/publications/characterising-rna-secondary-structure-space-using-information-entropy(2d736e45-c4f5-4682-bc7a-f5b8ab1a4262).html
Autor:
Ingolfur Edvardsson, Adam Novak, Preeti Arunapuram, Zsuzsanna Sükösd, Michael Golden, Jotun Hein, James W. J. Anderson
Publikováno v:
Arunapuram, P, Edvardsson, I, Golden, M, Anderson, J W J, Novák, A, Sükösd, Z & Hein, J 2013, ' StatAlign 2.0 : Combining statistical alignment with RNA secondary structure prediction ', Bioinformatics, vol. 29, no. 5, pp. 654-655 . https://doi.org/10.1093/bioinformatics/btt025
Motivation: Comparative modeling of RNA is known to be important for making accurate secondary structure predictions. RNA structure prediction tools such as PPfold or RNAalifold use an aligned set of sequences in predictions. Obtaining a multiple ali
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8452f1de58a0e393c928198606685a08
https://pure.au.dk/portal/da/publications/statalign-20(0932580b-0195-4fdd-a684-af275bf6c6d2).html
https://pure.au.dk/portal/da/publications/statalign-20(0932580b-0195-4fdd-a684-af275bf6c6d2).html
Publikováno v:
Sükösd, Z, Knudsen, B, Kjems, J & Pedersen, C N S 2012, ' PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data ', Bioinformatics, vol. 28, no. 20, pp. 2691-2692 . https://doi.org/10.1093/bioinformatics/bts488
Summary: PPfold is a multi-threaded implementation of the Pfold algorithm for RNA secondary structure prediction. Here we present a new version of PPfold, which extends the evolutionary analysis with a flexible probabilistic model for incorporating a
Autor:
Stephen C. Harvey, Zsuzsanna Sükösd, M. Shel Swenson, Prashant Gaurav, David A. Bader, Joshua Anderson, Christine E. Heitsch, Andrew Ash
Publikováno v:
BMC Research Notes
Swenson, M S, Anderson, J, Ash, A, Gaurav, P, Sükösd, Z, Bader, D A, Harvey, S C & Heitsch, C E 2012, ' GTfold: Enabling parallel RNA secondary structure prediction on multi-core desktops ', BMC Research Notes, vol. 5, no. 341 . https://doi.org/10.1186/1756-0500-5-341
Swenson, M S, Anderson, J, Ash, A, Gaurav, P, Sükösd, Z, Bader, D A, Harvey, S C & Heitsch, C E 2012, ' GTfold: Enabling parallel RNA secondary structure prediction on multi-core desktops ', BMC Research Notes, vol. 5, no. 341 . https://doi.org/10.1186/1756-0500-5-341
Accurate and efficient RNA secondary structure prediction remains an important open problem in computational molecular biology. Historically, advances in computing technology have enabled faster and more accurate RNA secondary structure predictions.
Publikováno v:
BMC Bioinformatics, Vol 12, Iss 1, p 103 (2011)
BMC Bioinformatics
Sükösd, Z, Knudsen, B, Værum, M, Kjems, J & Andersen, E S 2011, ' Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars ', B M C Bioinformatics, vol. 12, no. 103 . https://doi.org/10.1186/1471-2105-12-103
BMC Bioinformatics
Sükösd, Z, Knudsen, B, Værum, M, Kjems, J & Andersen, E S 2011, ' Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars ', B M C Bioinformatics, vol. 12, no. 103 . https://doi.org/10.1186/1471-2105-12-103
Background The prediction of the structure of large RNAs remains a particular challenge in bioinformatics, due to the computational complexity and low levels of accuracy of state-of-the-art algorithms. The pfold model couples a stochastic context-fre
Publikováno v:
Technical University of Denmark Orbit
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=dedup_wf_001::c8541b5ac97ff7ea18ce7942ac13ae32
https://orbit.dtu.dk/en/publications/1c03444c-5823-4920-b1e3-eb61fd107056
https://orbit.dtu.dk/en/publications/1c03444c-5823-4920-b1e3-eb61fd107056