Andronescu Mirela, Bereg Vera, Hoos Holger H, Condon Anne
Department of Computer Science, University of British Columbia, 2366 Main Mall, Vancouver, BC, Canada.
BMC Bioinformatics. 2008 Aug 13;9:340. doi: 10.1186/1471-2105-9-340.
The ability to access, search and analyse secondary structures of a large set of known RNA molecules is very important for deriving improved RNA energy models, for evaluating computational predictions of RNA secondary structures and for a better understanding of RNA folding. Currently there is no database that can easily provide these capabilities for almost all RNA molecules with known secondary structures.
In this paper we describe RNA STRAND - the RNA secondary STRucture and statistical ANalysis Database, a curated database containing known secondary structures of any type and organism. Our new database provides a wide collection of known RNA secondary structures drawn from public databases, searchable and downloadable in a common format. Comprehensive statistical information on the secondary structures in our database is provided using the RNA Secondary Structure Analyser, a new tool we have developed to analyse RNA secondary structures. The information thus obtained is valuable for understanding to which extent and with which probability certain structural motifs can appear. We outline several ways in which the data provided in RNA STRAND can facilitate research on RNA structure, including the improvement of RNA energy models and evaluation of secondary structure prediction programs. In order to keep up-to-date with new RNA secondary structure experiments, we offer the necessary tools to add solved RNA secondary structures to our database and invite researchers to contribute to RNA STRAND.
RNA STRAND is a carefully assembled database of trusted RNA secondary structures, with easy on-line tools for searching, analyzing and downloading user selected entries, and is publicly available at http://www.rnasoft.ca/strand.
对于推导改进的RNA能量模型、评估RNA二级结构的计算预测以及更好地理解RNA折叠而言，访问、搜索和分析大量已知RNA分子的二级结构的能力非常重要。目前，尚无数据库能够轻松地为几乎所有具有已知二级结构的RNA分子提供这些功能。
在本文中，我们描述了RNA STRAND——RNA二级结构与统计分析数据库，这是一个精心策划的数据库，包含任何类型和生物体的已知二级结构。我们的新数据库提供了从公共数据库中提取的大量已知RNA二级结构，可通过通用格式进行搜索和下载。我们使用RNA二级结构分析仪（这是我们开发的一种用于分析RNA二级结构的新工具），提供了关于我们数据库中二级结构的全面统计信息。由此获得的信息对于理解某些结构基序在何种程度上以及以何种概率出现非常有价值。我们概述了RNA STRAND中提供的数据可以促进RNA结构研究的几种方式，包括改进RNA能量模型和评估二级结构预测程序。为了跟上新的RNA二级结构实验的步伐，我们提供了必要的工具，以便将已解析的RNA二级结构添加到我们的数据库中，并邀请研究人员为RNA STRAND做出贡献。
RNA STRAND是一个精心组装的、可信的RNA二级结构数据库，具有方便的在线工具，用于搜索、分析和下载用户选择的条目，可在http://www.rnasoft.ca/strand上公开获取。
