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A partition function algorithm for nucleic acid secondary structure including pseudoknots
Author(s) -
Dirks Robert M.,
Pierce Niles A.
Publication year - 2003
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.10296
Subject(s) - nucleic acid , algorithm , nucleic acid secondary structure , computer science , nucleic acid structure , partition (number theory) , function (biology) , computational biology , mathematics , biology , combinatorics , genetics , rna , gene
Nucleic acid secondary structure models usually exclude pseudoknots due to the difficulty of treating these nonnested structures efficiently in structure prediction and partition function algorithms. Here, the standard secondary structure energy model is extended to include the most physically relevant pseudoknots. We describe an O ( N 5 ) dynamic programming algorithm, where N is the length of the strand, for computing the partition function and minimum energy structure over this class of secondary structures. Hence, it is possible to determine the probability of sampling the lowest energy structure, or any other structure of particular interest. This capability motivates the use of the partition function for the design of DNA or RNA molecules for bioengineering applications. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1664–1677, 2003