Kim Namhee, Shin Jin Sup, Elmetwaly Shereef, Gan Hin Hark, Schlick Tamar
Department of Chemistry, New York University, 100 Washington Square East, New York 10003, USA.
Bioinformatics. 2007 Nov 1;23(21):2959-60. doi: 10.1093/bioinformatics/btm439. Epub 2007 Sep 13.
Our RNA-As-Graph-Pools (RagPools) web server offers a theoretical companion tool for RNA in vitro selection and related problems. Specifically, it suggests how to construct RNA sequence/structure pools with user-specified properties and assists in analyzing resulting distributions. This utility follows our recently developed approach for engineering sequence pools that links RNA sequence space regions with corresponding structural distributions via a 'mixing matrix' approach combined with a graph theory analysis of RNA secondary-structure space; the mixing matrix specifies nucleotide transition rates, and graph theory links sequences to simple graphical objects representing RNA motifs. The companion RagPools web server ('Designer' component) provides optimized starting sequences, mixing matrices and associated weights in response to a user-specified target pool structure distribution. In addition, RagPools ('Analyzer' component) analyzes the motif distribution of pools generated from user-specified starting sequences and mixing matrices. Thus, RagPools serves as a guide to researchers who aim to synthesize RNA pools with desired properties and/or experiment in silico with various designs by our approach.
The web server is accessible on the web at http://rubin2.biomath.nyu.edu
我们的RNA-As-Graph-Pools（RagPools）网络服务器为RNA体外筛选及相关问题提供了一个理论辅助工具。具体而言，它能提示如何构建具有用户指定特性的RNA序列/结构库，并协助分析所得分布。该实用工具遵循我们最近开发的工程序列库方法，该方法通过“混合矩阵”方法并结合RNA二级结构空间的图论分析，将RNA序列空间区域与相应的结构分布联系起来；混合矩阵指定核苷酸转换率，图论将序列与代表RNA基序的简单图形对象联系起来。配套的RagPools网络服务器（“设计器”组件）根据用户指定的目标库结构分布提供优化的起始序列、混合矩阵和相关权重。此外，RagPools（“分析器”组件）分析从用户指定的起始序列和混合矩阵生成的库的基序分布。因此，RagPools为旨在合成具有所需特性的RNA库和/或通过我们的方法进行各种计算机模拟实验的研究人员提供了指导。
该网络服务器可通过网页http://rubin2.biomath.nyu.edu访问
