Supporting RNAstructure: Software for RNA Analysis

描述（申请人提供）：RNA在细胞功能中起着许多重要作用。在生物学的中心法则中，RNA是遗传信息的短暂载体，也是读取密码的适配分子。RNA催化反应，并在转录后基因调控、发育和免疫中发挥作用。RNA也在人类疾病中发挥作用，包括Prader-Willi和肌强直性营养不良。理解和利用RNA的力量，例如使用RNAi、反义技术或治疗性核酶，需要了解这些RNA序列的结构。RNAstructure是一个用于RNA二级结构预测和分析的软件包。它可以在http://rna.urmc.rochester.edu上找到，总共有超过11,000名用户下载了它。本提案的具体目标包括RNA结构包的开发和维护：1)开发用于RNA二级结构形成的焓最近邻参数，以便在其他温度下进行结构预测和分析。2)构建web服务器，提供RNA二级结构最近邻参数，并提供使用教程。3)在现有软件中增加RNAML支持，提高与其他软件包的互操作性。4)使用Java运行时库将RNAstructure移植到Unix、Linux和Macintosh OS X上，以构建用户界面。5)直接从RNAstructure中提供高质量的adobeacrobat文件（pdf）输出，以便可以编辑预测的结构以供出版。6)更新64位Microsoft Windows Vista的RNAstructure。7)在开放许可下提供源代码供下载。8)构建一个web服务器，用于预测与RNA目标的平衡结合亲和力的OligoWalk算法。Web服务器非常受欢迎，因为它易于使用。9)为RNAstructure用户社区提供一个电子邮件反射器。这项工作对人类健康具有广泛的影响。RNA结构中包含的计算机工具被其他人用来确定作为良好药物靶点的RNA序列。rna结构对于基于rna的药物的设计也很有用。

DESCRIPTION (provided by applicant): RNA plays many important roles in cellular function. In the Central Dogma of Biology, RNA serves as a transient carrier of genetic information and as the adapter molecule that reads the code. RNA catalyzes reactions and serves in post-transcriptional gene regulation, development, and immunity. RNA also plays roles in human disease, including Prader-Willi and myotonic dystrophy. Understanding and harnessing the power of RNA, e.g. with RNAi, antisense technology, or with therapeutic ribozymes, requires an understanding of the structures of these RNA sequences. RNAstructure is a software package for RNA secondary structure prediction and analysis. It is available at: http://rna.urmc.rochester.edu and has been downloaded by a total of over 11,000 users. The specific aims of this proposal include both development and maintenance for the RNAstructure package: 1) Develop enthalpy nearest neighbor parameters for RNA secondary structure formation to allow structure prediction and analysis at other temperatures. 2) Construct a web server to provide RNA secondary structure nearest neighbor parameters and offer tutorials on their use. 3) Add RNAML support to the existing software to improve interoperability with other software packages. 4) Port RNAstructure to Unix, Linux, and Macintosh OS X using the Java runtime library to build a user-interface. 5) Provide high quality Adobe Acrobat File (pdf) output directly from RNAstructure, so that predicted structures can be edited for publication. 6) Update RNAstructure for 64-bit Microsoft Windows Vista. 7) Provide source code for download under an open license. 8) Construct a web server for the OligoWalk algorithm for predicting equilibrium binding affinities to an RNA target. Web servers are highly popular because of there ease of use. 9) Offer an email reflector for communication by the RNAstructure user community. This work has broad implications for human health. The computer tools contained in RNAstructure are used by others to determine RNA sequences that are good drug targets. RNAstructure is also useful for the design of RNA-based Pharmaceuticals.