Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Prague, Czech Republic.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W42-8. doi: 10.1093/nar/gks560. Epub 2012 Jun 11.
The recent discoveries of regulatory non-coding RNAs changed our view of RNA as a simple information transfer molecule. Understanding the architecture and function of active RNA molecules requires methods for comparing and analyzing their 3D structures. While structural alignment of short RNAs is achievable in a reasonable amount of time, large structures represent much bigger challenge. Here, we present the SETTER web server for the RNA structure pairwise comparison utilizing the SETTER (SEcondary sTructure-based TERtiary Structure Similarity Algorithm) algorithm. The SETTER method divides an RNA structure into the set of non-overlapping structural elements called generalized secondary structure units (GSSUs). The SETTER algorithm scales as O(n(2)) with the size of a GSSUs and as O(n) with the number of GSSUs in the structure. This scaling gives SETTER its high speed as the average size of the GSSU remains constant irrespective of the size of the structure. However, the favorable speed of the algorithm does not compromise its accuracy. The SETTER web server together with the stand-alone implementation of the SETTER algorithm are freely accessible at http://siret.cz/setter.
最近发现的调控非编码 RNA 改变了我们对 RNA 作为一种简单信息传递分子的看法。要理解活性 RNA 分子的结构和功能，就需要有比较和分析其 3D 结构的方法。虽然短 RNA 的结构比对在合理的时间内是可行的，但对于较大的结构则是一个更大的挑战。在这里，我们介绍了 SETTER 网络服务器，用于利用 SETTER（基于二级结构的三级结构相似性算法）算法进行 RNA 结构的两两比较。SETTER 方法将 RNA 结构划分为称为广义二级结构单元 (GSSU) 的不重叠结构元素集。SETTER 算法的规模与 GSSU 的大小呈 O(n^2) 关系，与结构中的 GSSU 数量呈 O(n) 关系。这种规模使得 SETTER 具有很高的速度，因为 GSSU 的平均大小与结构的大小无关。然而，算法的快速性并没有影响其准确性。SETTER 网络服务器以及 SETTER 算法的独立实现可在 http://siret.cz/setter 上免费访问。
