Project Details
Projekt
Computational Detection of Bacterial ncRNAs and their Targets
Subject Area
Bioinformatics and Theoretical Biology
Term
from 2007 to 2014
Project identifier
Deutsche Forschungsgemeinschaft (DFG) - Project number 39932908
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 inuence of other regulatory elements and the detection of further features inuencing sRNA-mRNA interactions. Since kinetic effects can have a strong inuence 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.
DFG Programme
Priority Programmes
Subproject of
SPP 1258:
Sensory and Regulatory RNAs in Prokaryotes
