DFG-Projekt: Computational Detection of Bacterial ncRNAs and their Targets

Description of the project:
- no english description available -

In this project, we want improve the functional prediction of sRNA by first improving the interaction prediction, and second, by considering additional regulatory elements. Concerning current approaches for the prediction of RNA-RNA interactions, there are several problems and limitations that will be dealt with in our project. First, we will improve the determination of transcript boundaries, since the folding quite strongly depends on the exact ends of the input sequence. Second, current interaction prediction tools suffer from a low specificity. We will therefore apply different techniques to improve the specificity such as the use of conservation information, the influence of other regulatory elements and the detection of further features influencing sRNA-mRNA interaction. Since kinetic effects can have a strong influence of RNA folding, we will explore this effect in detail for RNA-RNA interactions. Finally, the best models for interaction prediction are currently computationally too complex to be used on a regular basis. We will therefore improve the efficiency of these approaches.

contact person: Prof. Dr. Rolf Backofen
Phone: 0049 761 203 7461
Email: backofen@informatik.uni-freiburg.de
Start of project: 01.06.2010
End of project: 31.05.2013
Project Management:
Albert-Ludwigs-University Freiburg
Prof. Dr. Rolf Backofen
Prof. Dr. Rolf Backofen
Georges-Köhler-Allee 106
79110 Freiburg

Phone: +49 (0) 761-203-7461
Fax: +49 (0) 761-203-7462
Email: backofen@informatik.uni-freiburg.de
Actual Research Report