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J Math Biol. 2008 Jan;56(1-2):129-44. Epub 2007 Jul 5.

Variations on RNA folding and alignment: lessons from Benasque.

Author information

1
Zentralfriedhof Wien, 3. Tor Simmeringer Haupstrasse, Wien, Austria.

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.

PMID:
17611759
DOI:
10.1007/s00285-007-0107-5
[Indexed for MEDLINE]

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