Genomics | Bioinformatics | Structure: RNA | Theory & Simulation | Structural Genomics
Predicting conserved interactions/structures of multiple alignments of RNA sequences
Stefan E Seemann*, Andreas S Richter, Peter Menzel, Tanja Gesell, Rolf Backhofen, Jan Gorodkin
*Corresponding author: Stefan E Seemann
Center for non-coding RNA in Technology and Health, IBHV, University of Copenhagen, Copenhagen, Denmark
F1000Posters 2011, 2: 1365 (poster) [ENGLISH]
19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology 2011 (ISMB/ECCB), 17 - 19 Jul 2011, L17
The function of non-coding RNA genes largely depends on their secondary structure and the interaction with other molecules. Thus, an accurate prediction of the secondary structure and RNA-RNA interaction is essential to understand the biological roles and pathways associated with a specific RNA gene. The RNA structure is constrained by thermodynamic energies and evolutionary conservation patterns.
Here, both information sources are unified in one scoring scheme by the Probabilistic Evolutionary and Thermodynamic (PET) model for analyzing multiple aligned RNA sequences for common RNA structure and for RNA interaction sites.
We present the predictor PETcofold, an extension of PETfold for RNA-RNA interactions, and its application on bacterial small RNAs, and snoRNAs and their targets. Additionally, we provide a web server with direct access to annotated RNA alignments to overcome the main drawback of the current methods that the prediction accuracy is largely dependent from the quality of the input alignment(s).
No relevant conflicts of interest declared.
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