A partition function algorithm for nucleic acid secondary structure including pseudoknots
A partition function algorithm for nucleic acid secondary structure including pseudoknots
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DOI：
10.1002/jcc.10296
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发表时间：
2003-10-01
影响因子：
3
通讯作者：
Pierce, NA
中科院分区：
文献类型：
--
作者：
Dirks, RM;Pierce, NA
由于在结构预测和配分函数算法中很难有效地处理这些非嵌套结构，因此核酸二级结构模型通常不包括伪结。在这里，标准的二级结构能量模型扩展到包括最物理相关的伪结。我们描述了一个O（N-5）的动态规划算法，其中N是链的长度，用于计算这类二级结构上的配分函数和最小能量结构。因此，可以确定对最低能量结构或任何其他特别感兴趣的结构进行采样的概率。这种能力促使使用分配函数来设计用于生物工程应用的DNA或RNA分子。(C)2003 Wiley Periodicals，Inc.
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. (C) 2003 Wiley Periodicals, Inc.