Publications - Published papers

Please find below publications of our group. Currently, we list 500 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.

Design of Multi-Stable Nucleic Acid Sequences

Ingrid Abfalter, Christoph Flamm, Peter F. Stadler

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PREPRINT 03-018: [ PDF ]  [ PS ]

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Proceedings of the German Conference on Bioinformatics. Volume I. H.-W. Mewes, V. Heun, D. Frishman, S. Kramer (Eds.), belleville Verlag Michael Farin, München, 2003, p.1-7.

Abstract


RNA molecules that can fold into to or more predefined alternative metastable structures can be designed rationally. We outline an algorithm for this task that reduces the problem to vertex coloring the union of all prescribed outerplanar secondary structure graphs. Starting from an ear decomposition of this composite graph colorings are produced by a dynamic programming procedure. Sequences can then be optimized for particular properties by means of standard optimization heuristics.