Publications - Published papers
Please find below publications of our group. Currently, we list 565 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 (
) is restricted to our local network and chosen collaborators.
If you have problems accessing electronic information, please let us know:
) 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.
Variations on RNA Folding and Alignment: Lessons from Benasque
Athanasius F. Bompfünewerer, Rolf Backofen, Stephan H. Berhart, Jana Hertel, Ivo L. Hofacker, Peter F. Stadler, Sebastian Will
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Status: Published
J Math Biol. 56: 129-144 (2008).
Abstract
Dynamic Programming Algorithms solve many standard problems of
RNA bioinformatics in polynomial time. In this contribution we discuss a series of
variations on these standard methods that implement refined biophysical models,
such as a restriction of RNA folding to canonical structures, and an extension of
structural alignments to an explicit scoring of stacking propensities. Furthermore,
we demonstrate that a local structural alignment can be employed for ncRNA gene
finding. In this context we discuss scanning variants for folding and alignment
algorithms.
Keywords
RNA folding, Secondary structure Alignment, Dynamic Programming
Note
10.1007/s00285-007-0107-5