RNASAlign：RNA 结构比对系统。

RNASAlign: RNA structural alignment system.

机构信息

Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong.

出版信息

Bioinformatics. 2011 Aug 1;27(15):2151-2. doi: 10.1093/bioinformatics/btr338. Epub 2011 Jun 8.

DOI:10.1093/bioinformatics/btr338

PMID:21659321

Abstract

MOTIVATION

Structural alignment of RNA is found to be a useful computational technique for idenitfying non-coding RNAs (ncRNAs). However, existing tools do not handle structures with pseudoknots. Although algorithms exist that can handle structural alignment for different types of pseudoknots, no software tools are available and users have to determine the type of pseudoknots to select the appropriate algoirthm to use which limits the usage of structural alignment in identifying novel ncRNAs.

RESULTS

We implemented the first web server, RNASAlign, which can automatically identify the pseudoknot type of a secondary structure and perform structural alignment of a folded RNA with every region of a target DNA/RNA sequence. Regions with high similarity scores and low e-values, together with the detailed alignments will be reported to the user. Experiments on more than 350 ncRNA families show that RNASAlign is effective.

AVAILABILITY

http://www.bio8.cs.hku.hk/RNASAlign.

摘要

动机

RNA 的结构比对被发现是一种识别非编码 RNA(ncRNAs) 的有用计算技术。然而，现有的工具无法处理具有假结的结构。虽然存在可以处理不同类型假结结构比对的算法，但没有可用的软件工具，用户必须确定假结的类型，以选择合适的算法来使用，这限制了结构比对在识别新的 ncRNAs 中的应用。

结果

我们实现了第一个 Web 服务器 RNASAlign，它可以自动识别二级结构的假结类型，并对折叠的 RNA 与目标 DNA/RNA 序列的每个区域进行结构比对。具有高相似度得分和低 e 值的区域，以及详细的比对结果将报告给用户。对 350 多个 ncRNA 家族的实验表明，RNASAlign 是有效的。