Moments of the Boltzmann distribution for RNA secondary structures
Moments of the Boltzmann distribution for RNA secondary structures
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DOI：
10.1016/j.bulm.2004.12.003
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发表时间：
2005-09-01
影响因子：
3.5
通讯作者：
Nagy, B
中科院分区：
文献类型：
--
作者：
Miklós, I;Meyer, IM;Nagy, B
我们提出了一种动态规划算法，它能够计算RNA二级结构的玻尔兹曼分布的任意矩。我们已经在一个名为RNA-Variance的程序中实现了该算法，并研究了生物RNA序列和随机RNA序列的Boltzmann分布之间的差异。我们发现，在玻耳兹曼分布中，生物序列的最小自由能结构比随机序列具有更高的概率。此外，我们还证明了生物序列的自由能比随机序列具有更小的方差，生物序列的最小自由能比随机序列的最小自由能更接近其余结构的期望自由能。这些结果表明，具有生物功能的RNA序列不仅需要一个热力学稳定的最小自由能结构，而且还需要一个自由能接近最小自由能的结构集合。(C)2005年数学生物学学会。爱思唯尔有限公司出版。保留所有权利。
We here present a dynamic programming algorithm which is capable of calculating arbitrary moments of the Boltzmann distribution for RNA secondary structures. We have implemented the algorithm in a program called RNA-VARIANCE and investigate the difference between the Boltzmann distribution of biological and random RNA sequences. We find that the minimum free energy structure of biological sequences has a higher probability in the Boltzmann distribution than random sequences. Moreover, we show that the free energies of biological sequences have a smaller variance than random sequences and that the minimum free energy of biological sequences is closer to the expected free energy of the rest of the structures than that of random sequences. These results suggest that biologically functional RNA sequences not only require a thermodynamically stable minimum free energy structure, but also an ensemble of structures whose free energies are close to the minimum free energy. (c) 2005 Society for Mathematical Biology. Published by Elsevier Ltd. All rights reserved.