Abstract
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.
This work was supported by the Korea Science and Engineering Foundation (KOSEF) under grant R01-2003-000-10461-0.
Chapter PDF
Similar content being viewed by others
Keywords
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.
References
Lander, E.S.: Array of hope. Nature Genetics 21, 3–4 (1999)
De Rijk, P., Wuyts, J., De Wachter, R.: RnaViz 2: an improved representation of RNA secondary structure. Bioinformatics 19, 299–300 (2003)
Han, K., Kim, D., Kim, H.-J.: A vector-based method for drawing RNA secondary structure. Bioinformatics 15, 186–197 (1999)
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)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Byun, Y., Han, K. (2005). DNA Secondary Structures for Probe Design. In: Pach, J. (eds) Graph Drawing. GD 2004. Lecture Notes in Computer Science, vol 3383. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-31843-9_53
Download citation
DOI: https://doi.org/10.1007/978-3-540-31843-9_53
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-24528-5
Online ISBN: 978-3-540-31843-9
eBook Packages: Computer ScienceComputer Science (R0)