SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework

Irmtraud M Meyer; István Miklós

doi:10.1371/journal.pcbi.0030149

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Open Access

Peer-reviewed

Research Article

SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework

Irmtraud M Meyer ,

*To whom correspondence should be addressed. E-mail: irmtraud.meyer@cantab.net

Affiliations UBC Bioinformatics Centre, University of British Columbia, Vancouver, British Columbia, Canada , Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
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István Miklós

Affiliations Alfréd Rényi Institute of Mathematics, Hungarian Academy of Sciences, Budapest, Hungary , Computer and Automation Research Institute (MTA-SZTAKI), Hungarian Academy of Sciences, Budapest, Hungary , eScience Regional Knowledge Centre, Eötvös Loránd University, Budapest, Hungary
⨯

SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework

Irmtraud M Meyer,
István Miklós

Published: August 10, 2007
https://doi.org/10.1371/journal.pcbi.0030149

About the Authors

Irmtraud M Meyer

*To whom correspondence should be addressed. E-mail: irmtraud.meyer@cantab.net

Affiliations UBC Bioinformatics Centre, University of British Columbia, Vancouver, British Columbia, Canada , Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada

István Miklós

Affiliations Alfréd Rényi Institute of Mathematics, Hungarian Academy of Sciences, Budapest, Hungary , Computer and Automation Research Institute (MTA-SZTAKI), Hungarian Academy of Sciences, Budapest, Hungary , eScience Regional Knowledge Centre, Eötvös Loránd University, Budapest, Hungary

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

IMM and IM conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, and wrote the paper.

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RNA structure
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RNA alignment
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Sequence alignment
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Multiple alignment calculation
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RNA structure prediction
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Phylogenetic analysis
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Pseudoknots
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RNA sequences
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