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RNA-DV: an interactive tool for editing and visualizing RNA secondary structures

Authors:

Herbert H. Tsang,

Denny C. DaiAuthors Info & Claims

BCB '12: Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine

Pages 601 - 603

https://doi.org/10.1145/2382936.2383036

Published: 07 October 2012 Publication History

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Abstract

Although many tools were developed for visualization of RNA secondary structure, RNA-DV is a tool which provides a flexible and powerful interface for RNA secondary structure design and visualization. Being able to dynamically make modification and visualize the result is the most significant contribution of RNA-DV. The ability to allow researcher to make edit and visualize the resulting structure help set apart RNA-DV from other existing tools. The structural modification is achieved through a combination of mouse and keyboard operations. The direct and intuitive interface allows the structure prediction researcher to visualize the structure. Furthermore, RNA-DV provides the necessary tool for structure designers to explore the effect of various structural elements in terms of thermodynamic contributions. Four different thermodynamic energy models (efn2, HotKnots, Major and RNAeval) were incorporated allowing users to observe real-time energy changes while designing the structure. Visualizing and editing of pseudo-knotted structure is also supported in RNA-DV.

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Cited By

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Tsang H(2024)Simulated Annealing for RNA Design with SIMARDRNA Design10.1007/978-1-0716-4079-1_6(95-108)Online publication date: 3-Jul-2024
https://doi.org/10.1007/978-1-0716-4079-1_6
Hampson DWiebe TTsang H(2019)Comparison of Two Folding Functions for RNA Secondary Structure Design2019 IEEE Symposium Series on Computational Intelligence (SSCI)10.1109/SSCI44817.2019.9002762(2946-2953)Online publication date: Dec-2019
https://doi.org/10.1109/SSCI44817.2019.9002762
Hampson DTsang H(2018)Incorporating Dynamic Exploration Strategy for RNA Design2018 IEEE Symposium Series on Computational Intelligence (SSCI)10.1109/SSCI.2018.8628681(1041-1048)Online publication date: Nov-2018
https://doi.org/10.1109/SSCI.2018.8628681
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Index Terms

RNA-DV: an interactive tool for editing and visualizing RNA secondary structures
1. Computing methodologies
  1. Computer graphics
    1. Graphics systems and interfaces
2. Information systems
  1. Information systems applications

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Information

Published In

BCB '12: Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine

October 2012

725 pages

ISBN:9781450316705

DOI:10.1145/2382936

General Chair:
Sanjay Ranka
University of Florida
,
Program Chairs:
Tamer Kahveci
University of Florida
,
Mona Singh
Princeton University

Publisher

Association for Computing Machinery

New York, NY, United States

Publication History

Published: 07 October 2012

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BCB' 12

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SIGBio

BCB' 12: ACM International Conference on Bioinformatics, Computational Biology and Biomedicine

October 7 - 10, 2012

Florida, Orlando

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BCB '12 Paper Acceptance Rate 33 of 159 submissions, 21%;

Overall Acceptance Rate 254 of 885 submissions, 29%

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Cited By

View all

Tsang H(2024)Simulated Annealing for RNA Design with SIMARDRNA Design10.1007/978-1-0716-4079-1_6(95-108)Online publication date: 3-Jul-2024
https://doi.org/10.1007/978-1-0716-4079-1_6
Hampson DWiebe TTsang H(2019)Comparison of Two Folding Functions for RNA Secondary Structure Design2019 IEEE Symposium Series on Computational Intelligence (SSCI)10.1109/SSCI44817.2019.9002762(2946-2953)Online publication date: Dec-2019
https://doi.org/10.1109/SSCI44817.2019.9002762
Hampson DTsang H(2018)Incorporating Dynamic Exploration Strategy for RNA Design2018 IEEE Symposium Series on Computational Intelligence (SSCI)10.1109/SSCI.2018.8628681(1041-1048)Online publication date: Nov-2018
https://doi.org/10.1109/SSCI.2018.8628681
Shabash BWiese K(2017)RNA VisualizationIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2016.252242114:3(696-712)Online publication date: 1-May-2017
https://dl.acm.org/doi/10.1109/TCBB.2016.2522421
Hampson DSav STsang H(2016)Investigation of Multi-Objective Optimization criteria for RNA design2016 IEEE Symposium Series on Computational Intelligence (SSCI)10.1109/SSCI.2016.7850232(1-8)Online publication date: Dec-2016
https://doi.org/10.1109/SSCI.2016.7850232
Grypma PBabbitt JTsang H(2013)A study on the effect of different thermodynamic models for predicting pseudoknotted RNA secondary structures2013 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)10.1109/CIBCB.2013.6595388(52-59)Online publication date: Apr-2013
https://doi.org/10.1109/CIBCB.2013.6595388

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Animal Actin Phylogeny and RNA Secondary Structure Study

Evolutionary rate variation and RNA secondary structure prediction

Asymptotics of Canonical RNA Secondary Structures