Computational Detection of Bacterial ncRNAs and their Targets

细菌 ncRNA 及其靶标的计算检测

• 批准号: 39932908
• 负责人: Professor Dr. Rolf Backofen
• 金额: --
• 依托单位: Lehrstuhl für Bioinformatik
• 依托单位国家: 德国
• 项目类别: Priority Programmes
• 财政年份: 2007
• 资助国家: 德国
• 起止时间: 2006-12-31 至 2013-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/39932908?language=en
• 关键词: Computational; Detection; Bacterial; ncRNAs; their

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.

在这个项目中，我们希望通过首先改善相互作用预测，其次，通过考虑额外的调控元件来改善sRNA的功能预测。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，当前的交互预测工具具有低特异性。因此，我们将应用不同的技术来提高特异性，例如使用保守信息，其他调控元件的影响和检测影响sRNA-mRNA相互作用的进一步特征。由于动力学效应对RNA折叠有很强的影响，我们将详细探讨这种效应对RNA-RNA相互作用的影响。最后，用于交互预测的最佳模型目前在计算上过于复杂，无法定期使用。因此，我们将提高这些方法的效率。