DNA Secondary Structures for Probe Design

  • Yanga Byun
  • Kyungsook Han
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3383)


Visualizing DNA secondary structures is essential to fast and efficient design of probes for DNA chips. There are several programs available for visualizing single-stranded RNA secondary structures, but these programs cannot be used to draw DNA secondary structures formed by several hundred to thousand primers and target genes. We have developed an algorithm and program for visualizing DNA secondary structures formed by multiple strands. We believe the program will be a valuable tool for designing primers and probes in DNA chips.


Secondary Structure Probe Design Input Data Format Loop Center Secondary Struc 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. 1.
    Lander, E.S.: Array of hope. Nature Genetics 21, 3–4 (1999)CrossRefGoogle Scholar
  2. 2.
    De Rijk, P., Wuyts, J., De Wachter, R.: RnaViz 2: an improved representation of RNA secondary structure. Bioinformatics 19, 299–300 (2003)CrossRefGoogle Scholar
  3. 3.
    Han, K., Kim, D., Kim, H.-J.: A vector-based method for drawing RNA secondary structure. Bioinformatics 15, 186–197 (1999)CrossRefGoogle Scholar
  4. 4.
    Matzura, O., Wennborg, A.: RNAdraw: an integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows. Computer Applications in the Biosciences 12, 247–249 (1996)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Yanga Byun
    • 1
  • Kyungsook Han
    • 1
  1. 1.School of Computer Science and EngineeringInha UniversityInchonKorea

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