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Stem Trace: an interactive visual tool for comparative RNA structure analysis.

W Kasprzak1, B Shapiro

  • 1Intramural Research Support Program, SAIC Frederick, National Cancer Institute/FCRDC, Bldg 469, Rm 150C, MD 21702, USA. kasprzak@ncifcrf.gov

Bioinformatics (Oxford, England)
|March 9, 1999
PubMed
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Stem Trace is a novel tool for analyzing RNA structures within the STRUCTURELAB workbench. It visually explores RNA folding data, revealing conserved structures in HIV sequences.

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Structural Biology

Background:

  • STRUCTURELAB is a computer workbench for RNA structure analysis.
  • RNA structure determination involves analyzing large databases of computationally generated structures.
  • Stem Trace offers a novel, visual, interactive, and exploratory approach to analyze this data.

Purpose of the Study:

  • To introduce Stem Trace, a new tool within STRUCTURELAB for RNA structure analysis.
  • To demonstrate the utility of Stem Trace in exploring and visualizing RNA structural data.
  • To showcase Stem Trace's capability in identifying conserved RNA structures.

Main Methods:

  • Stem Trace provides high-level graphical analysis.
  • It integrates with complementary visualization tools for orthogonal data views.

Related Experiment Videos

  • The tool can draw structures represented by a stem trace, acting as a graphical interface to an RNA structural database.

    • Main Results:

    • Stem Trace's capabilities are illustrated using RNA folding data from 24 HIV-1, HIV-2, and SIV strains.
    • Analysis focused on the HIV dimerization region, crucial for viral processes like reverse transcription and encapsidation.
    • Examples demonstrate Stem Trace's effectiveness in elucidating conserved structures across different HIV strains.

    Conclusions:

    • Stem Trace is a powerful, visually driven tool for RNA structure analysis.
    • It facilitates the exploration of large RNA structural datasets.
    • The tool aids in identifying and understanding conserved RNA structural elements, as shown in the HIV dimerization region analysis.