Journal
JOURNAL OF COMPUTATIONAL BIOLOGY
Volume 18, Issue 10, Pages 1339-1351Publisher
MARY ANN LIEBERT, INC
DOI: 10.1089/cmb.2010.0086
Keywords
algorithms; combinatorics; computational molecular biology; probability; strings
Categories
Funding
- ANR [ANR-06-BLAN-0045]
- Digiteo
- Agence Nationale de la Recherche (ANR) [ANR-06-BLAN-0045] Funding Source: Agence Nationale de la Recherche (ANR)
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In 2004, Condon and coauthors gave a hierarchical classification of exact RNA structure prediction algorithms according to the generality of structure classes that they handle. We complete this classification by adding two recent prediction algorithms. More importantly, we precisely quantify the hierarchy by giving closed or asymptotic formulas for the theoretical number of structures of given size n in all the classes but one. This allows us to assess the tradeoff between the expressiveness and the computational complexity of RNA structure prediction algorithms.
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