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This article is part of the supplement: Selected articles from the Eleventh Asia Pacific Bioinformatics Conference (APBC 2013): Bioinformatics

Open Access Proceedings

An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs

Tzu-Hao Chang1, Hsi-Yuan Huang2, Justin Bo-Kai Hsu2, Shun-Long Weng23456, Jorng-Tzong Horng789* and Hsien-Da Huang23*

Author Affiliations

1 Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei, Taiwan

2 Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan

3 Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan

4 Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, Taiwan

5 Mackay Medicine, Nursing and Management College, Taipei, Taiwan

6 Department of Medicine, Mackay Medical College, New Taipei City, Taiwan

7 Department of Computer Science and Information Engineering, National Central University, Chung-Li 320, Taiwan

8 Institute of Systems Biology and Bioinformatics, National Central University, Chung-Li 320, Taiwan

9 Department of Biomedical informatics, Asia University, Wufeng 413, Taiwan

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BMC Bioinformatics 2013, 14(Suppl 2):S4  doi:10.1186/1471-2105-14-S2-S4

Published: 21 January 2013

Abstract

Background

Functional RNA molecules participate in numerous biological processes, ranging from gene regulation to protein synthesis. Analysis of functional RNA motifs and elements in RNA sequences can obtain useful information for deciphering RNA regulatory mechanisms. Our previous work, RegRNA, is widely used in the identification of regulatory motifs, and this work extends it by incorporating more comprehensive and updated data sources and analytical approaches into a new platform.

Methods and results

An integrated web-based system, RegRNA 2.0, has been developed for comprehensively identifying the functional RNA motifs and sites in an input RNA sequence. Numerous data sources and analytical approaches are integrated, and several types of functional RNA motifs and sites can be identified by RegRNA 2.0: (i) splicing donor/acceptor sites; (ii) splicing regulatory motifs; (iii) polyadenylation sites; (iv) ribosome binding sites; (v) rho-independent terminator; (vi) motifs in mRNA 5'-untranslated region (5'UTR) and 3'UTR; (vii) AU-rich elements; (viii) C-to-U editing sites; (ix) riboswitches; (x) RNA cis-regulatory elements; (xi) transcriptional regulatory motifs; (xii) user-defined motifs; (xiii) similar functional RNA sequences; (xiv) microRNA target sites; (xv) non-coding RNA hybridization sites; (xvi) long stems; (xvii) open reading frames; (xviii) related information of an RNA sequence. User can submit an RNA sequence and obtain the predictive results through RegRNA 2.0 web page.

Conclusions

RegRNA 2.0 is an easy to use web server for identifying regulatory RNA motifs and functional sites. Through its integrated user-friendly interface, user is capable of using various analytical approaches and observing results with graphical visualization conveniently. RegRNA 2.0 is now available at http://regrna2.mbc.nctu.edu.tw webcite.