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

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題名:	An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs
作者:	洪炯宗;Chang, Tzu-Hao;Huang, Hsi-Yuan;Hsu, Justin Bo-Kai;Weng, Shun-Long;Horng, Jorng-Tzong;Huang, Hsien-Da
貢獻者:	資訊電機學院資訊工程學系
關鍵詞:	Algorithms;Base Sequence;Bioinformatics;Biomedical and Life Sciences;Computational Biology/Bioinformatics;Computer Appl. in Life Sciences;Computer Graphics;Gene expression;Gene Expression Regulation;Genomics;Internet;Life Sciences;Microarrays;Nucleotide Motifs;Proceedings;Protein synthesis;Regulatory Sequences, Nucleic Acid;Ribonucleic acid;RNA;Software;Studies;User-Computer Interface
日期:	2013-01-21
上傳時間:	2026-04-23 13:16:02 (UTC+8)
出版者:	BioMed Central Ltd.;London: Springer Science and Business Media LLC
摘要:	摘要： AbstractBackgroundFunctional 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 resultsAn 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.ConclusionsRegRNA 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 <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://regrna2.mbc.nctu.edu.tw" ext-link-type="uri">http://regrna2.mbc.nctu.edu.tw</jats:ext-link>. 其他題名： BMC Bioinformatics 出版者： London: Springer Science and Business Media LLC 出版日期： 2013-01-21 出處： BMC Bioinformatics, 2013-01, Vol.14 (S2), p.S4--S4, Article S4 資源來源： Publicly Available Content Database 版權： Chang et al.; licensee BioMed Central Ltd. 2013 This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License ( ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 版權： 2013 Chang et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 版權： Copyright ©2013 Chang et al.; licensee BioMed Central Ltd. 2013 Chang et al.; licensee BioMed Central Ltd. 識別號： ISSN: 1471-2105 識別號： EISSN: 1471-2105 識別號： DOI: 10.1186/1471-2105-14-s2-s4 識別號： PMID: 23369107
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