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Nucleic Acids Res. 2011 Jul;39(Web Server issue):W107-11. doi: 10.1093/nar/gkr248. Epub 2011 May 23.

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

Author information

1
Center for Non-coding RNA in Technology and Health, Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg, Denmark.

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/.

PMID:
21609960
PMCID:
PMC3125731
DOI:
10.1093/nar/gkr248
[Indexed for MEDLINE]
Free PMC Article

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