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Nucleic Acids Research 2006 34(Web Server issue):W423-W428; doi:10.1093/nar/gkl231
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

RNAMST: efficient and flexible approach for identifying RNA structural homologs

Tzu-Hao Chang1, Hsien-Da Huang2,3,4,*, Tzu-Neng Chuang1,5, Dray-Ming Shien1,6 and Jorng-Tzong Horng1,7,*

1 Department of Computer Science and Information Engineering, National Central University Chung-Li 320, Taiwan 2 Department of Biological Science and Technology, National Chiao Tung University Hsin-Chu 300, Taiwan 3 Institute of Bioinformatics, National Chiao Tung University Hsin-Chu 300, Taiwan 4 Core Facility for Structural Bioinformatics, National Chiao Tung University Hsin-Chu 300, Taiwan 5 Department of Electronic Engineering, Ching-Yun University Chung-Li 320, Taiwan 6 Department of Electronic Engineering, Chin Min Institute of Technology Miao-Li, Taiwan 7 Department of Life Science, National Central University Chung-Li 320, Taiwan

*To whom correspondence should be addressed. Tel: +886 3 5712121 (ext. 56952); Fax: +886 3 5729288; Email: bryan{at}mail.nctu.edu.tw

*Correspondence may also be addressed to Jorng-Tzong Horng. Fax: +886 3 4222681; Email: horng{at}db.csie.ncu.edu.tw

Received February 14, 2006. Revised March 4, 2006. Accepted March 27, 2006.

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/.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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