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Springer, Journal of Mathematical Biology, 1-2(56), p. 129-144, 2007

DOI: 10.1007/s00285-007-0107-5

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Variations on RNA Folding and Alignment: Lessons from Benasque

Journal article published in 2007 by Bompfünewerer Af, Athanasius F. Bompfünewerer, Rolf Backofen ORCID, Stephan H. Bernhart, Bernhart Sh, Jana Hertel, Ivo L. Hofacker, Hofacker Il, Stadler Pf, Peter F. Stadler ORCID, Sebastian Will
This paper is available in a repository.
This paper is available in a repository.

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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.