The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences

Ernst Stefan Seemann; Karl Peter Menzel; Rolf Backofen; Jan Gorodkin

doi:10.1093/nar/gkr248

The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences

Ernst Stefan Seemann, Karl Peter Menzel, Rolf Backofen, Jan Gorodkin

Computational and RNA Biology

20 Citations (Scopus)

Abstract

The function of non-coding RNA genes largely depends on their secondary structure and the interaction with other molecules. Thus, an accurate prediction of secondary structure and RNA-RNA interaction is essential for the understanding of biological roles and pathways associated with a specific RNA gene. We present web servers to analyze multiple RNA sequences for common RNA structure and for RNA interaction sites. The web servers are based on the recent PET (Probabilistic Evolutionary and Thermodynamic) models PETfold and PETcofold, but add user friendly features ranging from a graphical layer to interactive usage of the predictors. Additionally, the web servers provide direct access to annotated RNA alignments, such as the Rfam 10.0 database and multiple alignments of 16 vertebrate genomes with human. The web servers are freely available at: http://rth.dk/resources/petfold/

Original language	English
Journal	Nucleic Acids Research
Volume	39
Issue number	Suppl. 2
Pages (from-to)	W107-W111
Number of pages	5
ISSN	0305-1048
DOIs	https://doi.org/10.1093/nar/gkr248
Publication status	Published - 1 Jul 2011

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10.1093/nar/gkr248

Cite this

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title = "The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences",

abstract = "The function of non-coding RNA genes largely depends on their secondary structure and the interaction with other molecules. Thus, an accurate prediction of secondary structure and RNA-RNA interaction is essential for the understanding of biological roles and pathways associated with a specific RNA gene. We present web servers to analyze multiple RNA sequences for common RNA structure and for RNA interaction sites. The web servers are based on the recent PET (Probabilistic Evolutionary and Thermodynamic) models PETfold and PETcofold, but add user friendly features ranging from a graphical layer to interactive usage of the predictors. Additionally, the web servers provide direct access to annotated RNA alignments, such as the Rfam 10.0 database and multiple alignments of 16 vertebrate genomes with human. The web servers are freely available at: http://rth.dk/resources/petfold/",

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T1 - The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences

AU - Seemann, Ernst Stefan

AU - Menzel, Karl Peter

AU - Backofen, Rolf

AU - Gorodkin, Jan

PY - 2011/7/1

Y1 - 2011/7/1

N2 - The function of non-coding RNA genes largely depends on their secondary structure and the interaction with other molecules. Thus, an accurate prediction of secondary structure and RNA-RNA interaction is essential for the understanding of biological roles and pathways associated with a specific RNA gene. We present web servers to analyze multiple RNA sequences for common RNA structure and for RNA interaction sites. The web servers are based on the recent PET (Probabilistic Evolutionary and Thermodynamic) models PETfold and PETcofold, but add user friendly features ranging from a graphical layer to interactive usage of the predictors. Additionally, the web servers provide direct access to annotated RNA alignments, such as the Rfam 10.0 database and multiple alignments of 16 vertebrate genomes with human. The web servers are freely available at: http://rth.dk/resources/petfold/

AB - The function of non-coding RNA genes largely depends on their secondary structure and the interaction with other molecules. Thus, an accurate prediction of secondary structure and RNA-RNA interaction is essential for the understanding of biological roles and pathways associated with a specific RNA gene. We present web servers to analyze multiple RNA sequences for common RNA structure and for RNA interaction sites. The web servers are based on the recent PET (Probabilistic Evolutionary and Thermodynamic) models PETfold and PETcofold, but add user friendly features ranging from a graphical layer to interactive usage of the predictors. Additionally, the web servers provide direct access to annotated RNA alignments, such as the Rfam 10.0 database and multiple alignments of 16 vertebrate genomes with human. The web servers are freely available at: http://rth.dk/resources/petfold/

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DO - 10.1093/nar/gkr248

M3 - Journal article

C2 - 21609960

SN - 0305-1048

VL - 39

SP - W107-W111

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - Suppl. 2

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