Sequence and Structural Patterns in RNA

“这项奖励是根据2009年美国复苏和再投资法案（公法111-5）资助的。”普渡大学获得了一项资助，用于实现一个完整的信息学系统，用于识别保守的RNA结构拓扑，并在序列数据库中寻找类似拓扑的新示例。这将允许RNA研究人员进行假设/搜索/假设-改进的相同循环，这对DNA和蛋白质来说是如此强大。RNA在翻译、RNA剪接、基因调控和病毒感染等核心生化过程中起着核心作用。曾经被认为只是一个结构支架，现在人们认识到RNA也可以单独或在核糖核蛋白复合物中作为酶。然而，在理解RNA在细胞中的作用方面的进展一直受到实验确定和计算分析RNA结构的困难的阻碍。基于识别保守结构的方法在推断DNA和蛋白质的功能特性方面非常强大。这是因为正是分子的功能使序列在进化过程中显得保守。不幸的是，对RNA结构进行类似的分析是不可能的，因为保守作用在碱基对结构的水平上，而不是序列本身的水平上。由于许多其他生物学问题，如系统生物学、调节电路和某些类型的分子间结合，都有很强的图形成分，因此本项目开发的思想和软件将显著推进生物学研究的其他领域。图挖掘也是计算机科学和其他学科的一个重要课题，也可能从这项工作中受益。在这个项目中更广泛的影响活动包括三名博士研究生的研究，他们在生物学和计算机科学方面受过交叉训练，关于这个项目的各个方面。扩展到高中将包括RNA拓扑结构的模块。该项目的软件将公开发布：http://wiki.genomics.purdue.edu/index.php/Gribskov::Main

"This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5)."Purdue University is awarded a grant to implement a complete informatics system for identifying conserved RNA structure topologies, and for finding new examples of similar topologies in sequence databases. This will allow RNA researchers the same loop of hypothesis/search/hypothesis-refinement that has been so powerful for DNA and proteins.RNA plays a central role in core biochemical process such as translation, RNA-splicing, gene regulation, and viral infection. Once thought to be only a structural scaffold, it is now appreciated that RNA can also act as an enzyme on its own or in ribonucleoprotein complexes. However, advances in understanding the role that RNA plays in the cell has been hampered by the difficulty in experimentally determining and computationally analyzing RNA structures. Approaches based on identifying conserved structures have been extremely powerful in deducing functional properties of DNA and proteins. This is because it is the function of the molecule that makes the sequence appear conserved over evolutionary time. Unfortunately, a similar analysis has not been possible for RNA structures because the conservation acts at the level of the base-paired structure rather than that of sequence per se.Since many other biological problems, such as systems biology, regulatory circuits, and some kinds of intermolecular binding, have strong graphical components, the ideas and software developed in this project will significantly advance other areas of biological research. Graph mining is also an important subject in Computer Science and other disciplines, which may also benefit from this work.Broader impact activities during this project include the research of three PhD students, cross-trained in both Biology and Computer Science, on aspects of this project. Outreach to high schools will include modules on RNA topology structure. Software from this project will be made publically available: http://wiki.genomics.purdue.edu/index.php/Gribskov::Main