Variations on RNA folding and alignment: lessons from Benasque

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 exten...

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Bibliographic Details
Published in:Journal of mathematical biology Vol. 56; no. 1-2; pp. 129 - 144
Main Authors: Bompfünewerer, Athanasius F., Backofen, Rolf, Bernhart, Stephan H., Hertel, Jana, Hofacker, Ivo L., Stadler, Peter F., Will, Sebastian
Format: Journal Article
Language:English
Published: Berlin/Heidelberg Springer-Verlag 01.01.2008
Springer Nature B.V
Subjects:
Algorithms
Applications of Mathematics
Computational Biology - methods
Mathematical and Computational Biology
Mathematics
Mathematics and Statistics
Nucleic Acid Conformation
RNA, Untranslated - chemistry
RNA, Untranslated - genetics
Sequence Alignment
RNA folding
Secondary structure alignment
90C90
Dynamic programming
90C27
92C40
ISSN:0303-6812, 1432-1416
Online Access:Get full text
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Summary: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.
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ISSN:0303-6812
1432-1416
DOI:10.1007/s00285-007-0107-5