Sequence and Structural Patterns in RNA

“该奖项是根据2009年美国复苏和再投资法案（公法111-5）资助的。“普渡大学获得了一笔赠款，用于实施一个完整的信息学系统，用于识别保守的RNA结构拓扑结构，并在序列数据库中找到类似拓扑结构的新实例。 这将使RNA研究人员能够进行与DNA和蛋白质相同的假设/搜索/假设-改进循环。RNA在核心生物化学过程中起着核心作用，如翻译，RNA剪接，基因调控和病毒感染。 曾经认为RNA只是一种结构支架，现在认识到RNA也可以单独或在核糖核蛋白复合物中充当酶。 然而，理解RNA在细胞中所起作用的进展受到了实验确定和计算分析RNA结构的困难的阻碍。 基于鉴定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得序列在进化过程中显得保守。 不幸的是，类似的分析还没有可能的RNA结构，因为保守作用的水平上的碱基配对的结构，而不是序列本身，因为许多其他生物学问题，如系统生物学，调节电路，和某些种类的分子间结合，有强大的图形组件，在这个项目中开发的思想和软件将显着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，这些学科也可能从这项工作中受益。该项目期间更广泛的影响活动包括三名博士生的研究，他们在生物学和计算机科学方面进行了交叉培训。对高中的宣传将包括RNA拓扑结构模块。该项目的软件将通过以下网址提供：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