Improving the Portability and Performance of jViz.RNA – A Dynamic RNA Visualization Software

  • Boris Shabash
  • Kay Wiese
  • Edward Glen
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7632)

Abstract

In this paper, four methods were explored for improving the performance of jViz.RNA’s structure drawing algorithm when dealing with large sequences; First, the approximation based Barnes-Hut algorithm was explored. Second, the effects of using multithreading were measured. additionally, dynamic C libraries, which integrate C code into the JavaTM environment, were investigated. Finally, a technique termed structure recall was examined.

The results demonstrated that the use of the Barnes-Hut algorithm produced the most drastic improvements in run-time, but distorts the structure if too crude of an approximation is used. Multithreading and integration of C code proved to be favorable approaches since these improved the speed at which calculations are done, without distorting the structures.

jViz.RNA is available to download from http://jviz.cs.sfu.ca/.

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References

  1. 1.
    Barnes, J., Hut, P.: A hierarchical O(N log N) force-calculation algorithm. Nature 324(4), 446–449 (1986)CrossRefGoogle Scholar
  2. 2.
    Broccoleri, R.E., Heinrich, G.: An Improved Algorithm for Nucleic Acid Secondary Structure Display. Bioinformatics 4(1), 167–173 (1988)CrossRefGoogle Scholar
  3. 3.
    Darty, K., Denise, A., Ponty, Y.: Varna: Interactive drawing and editing of the rna secondary structure. Bioinformatics 25(15) (2009)Google Scholar
  4. 4.
    De Risjk, P., De Wachter, R.: Rnaviz, a program for the visualisation of rna secondary structure. Nucleic Acids Research 25(22), 4679–4684 (1997)CrossRefGoogle Scholar
  5. 5.
    Glen, E.: JVIZ.RNA - A Tool for Visual Comparison and Analysis of RNA Secondary Structures. Master’s thesis, Simon Fraser University (2007)Google Scholar
  6. 6.
    Han, K., Byun, Y.: PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots. Bioinformatics 25(11), 1435–1437 (2009)CrossRefGoogle Scholar
  7. 7.
    Hofacker, I.L.: Vienna RNA secondary structure server. Ivo L. Hofacker 31(13), 3429–3431 (2003)Google Scholar
  8. 8.
    Jossinet, F., Ludwig, T.E., Westhof, E.: Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels. Bioinformatics 26(16), 2057–2059 (2010)CrossRefGoogle Scholar
  9. 9.
    Jossinet, F., Westhof, E.: The RnamlView Project. Institut de biologie moleculaire et cellulaire du CNRSGoogle Scholar
  10. 10.
    NVIDIA®. CUDATMParallel Programming Made Easy (2011), http://www.nvidia.com/object/cuda_home_new.html
  11. 11.
  12. 12.
    Wiese, K.C., Glen, E.: jViz.Rna -a java tool for RNA secondary structure visualization. IEEE Transactions on NanoBioscience 4(3), 212–218 (2005)CrossRefGoogle Scholar
  13. 13.
    Wiese, K.C., Glen, E.: jViz.Rna - An Interactive Graphical Tool for Visualizing RNA Secondary Structure Including Pseudoknots. In: CBMS, pp. 659–664. IEEE Computer Society (2006)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Boris Shabash
    • 1
  • Kay Wiese
    • 1
  • Edward Glen
    • 1
  1. 1.School of Computing ScienceSimon Fraser UniversityBurnabyCanada

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