Abstract shapes of RNA
Abstract shapes of RNA
复制标题
DOI：
10.1093/nar/gkh779
复制
发表时间：
2004-01-01
影响因子：
14.9
通讯作者：
Rehmsmeier, M
中科院分区：
文献类型：
--
作者：
Giegerich, R;Voss, B;Rehmsmeier, M
非蛋白质编码RNA的功能通常由其结构决定。由于RNA结构的实验测定是耗时和昂贵的，其计算预测是非常感兴趣的，并且已知基于热力学参数的有效解决方案。然而，通常情况下，预测的最小自由能结构不是原生的，导致产生次优解的必要性。虽然这可以通过许多程序来实现，但用户经常面临类似结构的大量输出，尽管他或她对具有更基本差异的结构感兴趣，或者换句话说，具有不同的抽象形状。在这里，我们正式抽象形状的概念，并介绍其有效的计算。RNA分子的每种形状都包含一类相似的结构，并且在该类中具有最小自由能的代表性结构。形状分析在RNAshapes程序中实现。我们将RNAshapes应用于预测几种RNA的最佳和次佳抽象形状。对于给定的能量范围，形状的数量远小于结构的数量，并且在所有情况下，原生结构都是顶级形状代表之一。这表明研究人员可以快速专注于感兴趣的结构，而无需处理多达数千个接近最优的解决方案。我们补充这项研究的结构和形状空间的增长行为的大规模分析。RNAshapes可在比勒费尔德生物信息学服务器上下载和在线版本。
The function of a non-protein-coding RNA is often determined by its structure. Since experimental determination of RNA structure is time-consuming and expensive, its computational prediction is of great interest, and efficient solutions based on thermodynamic parameters are known. Frequently, however, the predicted minimum free energy structures are not the native ones, leading to the necessity of generating suboptimal solutions. While this can be accomplished by a number of programs, the user is often confronted with large outputs of similar structures, although he or she is interested in structures with more fundamental differences, or, in other words, with different abstract shapes. Here, we formalize the concept of abstract shapes and introduce their efficient computation. Each shape of an RNA molecule comprises a class of similar structures and has a representative structure of minimal free energy within the class. Shape analysis is implemented in the program RNAshapes. We applied RNAshapes to the prediction of optimal and suboptimal abstract shapes of several RNAs. For a given energy range, the number of shapes is considerably smaller than the number of structures, and in all cases, the native structures were among the top shape representatives. This demonstrates that the researcher can quickly focus on the structures of interest, without processing up to thousands of near-optimal solutions. We complement this study with a large-scale analysis of the growth behaviour of structure and shape spaces. RNAshapes is available for download and as an online version on the Bielefeld Bioinformatics Server.