Chang Tzu-Hao, Huang Hsien-Da, Chuang Tzu-Neng, Shien Dray-Ming, Horng Jorng-Tzong
Department of Computer Science and Information Engineering, National Central University, Chung-Li 320, Taiwan.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W423-8. doi: 10.1093/nar/gkl231.
RNA molecules fold into characteristic secondary structures for their diverse functional activities such as post-translational regulation of gene expression. Searching homologs of a pre-defined RNA structural motif, which may be a known functional element or a putative RNA structural motif, can provide useful information for deciphering RNA regulatory mechanisms. Since searching for the RNA structural homologs among the numerous RNA sequences is extremely time-consuming, this work develops a data preprocessing strategy to enhance the search efficiency and presents RNAMST, which is an efficient and flexible web server for rapidly identifying homologs of a pre-defined RNA structural motif among numerous RNA sequences. Intuitive user interface are provided on the web server to facilitate the predictive analysis. By comparing the proposed web server to other tools developed previously, RNAMST performs remarkably more efficiently and provides more effective and flexible functions. RNAMST is now available on the web at http://bioinfo.csie.ncu.edu.tw/~rnamst/.
RNA分子会折叠成具有特征性的二级结构，以实现其多样的功能活动，如基因表达的翻译后调控。搜索预定义RNA结构基序的同源物，该基序可能是已知的功能元件或假定的RNA结构基序，可为解读RNA调控机制提供有用信息。由于在众多RNA序列中搜索RNA结构同源物极其耗时，这项工作开发了一种数据预处理策略以提高搜索效率，并推出了RNAMST，这是一个高效且灵活的网络服务器，用于在众多RNA序列中快速识别预定义RNA结构基序的同源物。网络服务器上提供了直观的用户界面，以方便进行预测分析。通过将所提出的网络服务器与先前开发的其他工具进行比较，RNAMST的执行效率显著更高，并提供了更有效且灵活的功能。RNAMST现已在网页http://bioinfo.csie.ncu.edu.tw/~rnamst/ 上可用。
