Computational Detection of Bacterial ncRNAs and their Targets

在这个项目中，我们希望通过首先改进相互作用预测来改进sRNA的功能预测，其次，考虑额外的调控元件。关于目前预测RNA-RNA相互作用的方法，有几个问题和限制将在我们的项目中处理。首先，我们将改进转录本边界的确定，因为折叠非常强烈地依赖于输入序列的确切末端。其次，目前的相互作用预测工具的特异性较低。因此，我们将应用不同的技术来提高特异性，例如使用保护信息，其他调控元件的影响以及检测影响sRNA-mRNA相互作用的进一步特征。由于动力学效应可以对RNA折叠产生强烈的影响，我们将详细探讨RNA-RNA相互作用的这种效应。最后，目前用于相互作用预测的最佳模型在计算上过于复杂，无法定期使用。因此，我们将提高这些办法的效率。

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.