RiboSW - A web server for identifying RNA riboswitches

Tzu Hao Chang, Baw Jhiune Liu, Li Ching Wu, Hsien Da Huang, Chi Ta Yeh, Jorng Tzong Horng, Cheng Wei Chang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

Riboswitches are cis-acting genetic regulatory elements within a specific mRNA, and can regulate both transcription and translation by interacting with their corresponding metabolites. Recently, more and more riboswitches were identified and investigated about their roles in regulatory functions in different species. Both of the sequence contexts and structural conformations are important characteristics of riboswitches. None of previous developed tools, such Covariance Models (CMs), Riboswitch finder, and RibEx, provides a web server for efficiently searching homologous instances to known riboswitches and considers two crucial characteristics of each riboswitch, such as structural conformations and sequence contexts of functional regions. Therefore, we developed a systematic method to identify twelve kinds of riboswitches. The method is implemented and provided as a web server, RiboSW, to efficiently and conveniently identify riboswitches within messenger RNA sequences. RiboSW is now available on the web at http://bioinfo.csie.ncu.edu.tw/RiboSW/. The predictive accuracy of the proposed method is comparable with other previous tools. The efficiency of the proposed method for identifying riboswitches was improved in order to achieve a reasonable computational time required for the prediction. That makes it possible to have an accurate and convenient web server for biologists to obtain their analyzing results in a given mRNA sequence. The supplementary data is available on the web at http://bioinfo.csie.ncu.edu.tw/ RiboSW/sup.pdf.

Original languageEnglish
Title of host publicationProceedings of the 2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009
Pages260-265
Number of pages6
DOIs
Publication statusPublished - 2009
Externally publishedYes
Event2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009 - Taichung, Taiwan
Duration: Jun 22 2009Jun 24 2009

Other

Other2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009
CountryTaiwan
CityTaichung
Period6/22/096/24/09

Fingerprint

Riboswitch
RNA
Servers
Conformations
Transcription
Metabolites
Messenger RNA

ASJC Scopus subject areas

  • Information Systems
  • Biomedical Engineering
  • Health Informatics

Cite this

Chang, T. H., Liu, B. J., Wu, L. C., Huang, H. D., Yeh, C. T., Horng, J. T., & Chang, C. W. (2009). RiboSW - A web server for identifying RNA riboswitches. In Proceedings of the 2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009 (pp. 260-265). [5211268] https://doi.org/10.1109/BIBE.2009.12

RiboSW - A web server for identifying RNA riboswitches. / Chang, Tzu Hao; Liu, Baw Jhiune; Wu, Li Ching; Huang, Hsien Da; Yeh, Chi Ta; Horng, Jorng Tzong; Chang, Cheng Wei.

Proceedings of the 2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009. 2009. p. 260-265 5211268.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Chang, TH, Liu, BJ, Wu, LC, Huang, HD, Yeh, CT, Horng, JT & Chang, CW 2009, RiboSW - A web server for identifying RNA riboswitches. in Proceedings of the 2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009., 5211268, pp. 260-265, 2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009, Taichung, Taiwan, 6/22/09. https://doi.org/10.1109/BIBE.2009.12
Chang TH, Liu BJ, Wu LC, Huang HD, Yeh CT, Horng JT et al. RiboSW - A web server for identifying RNA riboswitches. In Proceedings of the 2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009. 2009. p. 260-265. 5211268 https://doi.org/10.1109/BIBE.2009.12
Chang, Tzu Hao ; Liu, Baw Jhiune ; Wu, Li Ching ; Huang, Hsien Da ; Yeh, Chi Ta ; Horng, Jorng Tzong ; Chang, Cheng Wei. / RiboSW - A web server for identifying RNA riboswitches. Proceedings of the 2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009. 2009. pp. 260-265
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