Efficient calculation of exact probability distributions of integer features on RNA secondary structures.
Efficient calculation of exact probability distributions of integer features on RNA secondary structures.
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DOI：
10.1186/1471-2164-15-s10-s6
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发表时间：
2014
期刊：
影响因子：
4.4
通讯作者：
Asai K
中科院分区：
文献类型：
--
作者：
Mori R;Hamada M;Asai K
尽管对RNA二级结构分析的需求不断增加，但RNA二级结构的预测并不总是可靠的。由于RNA可能具有复杂的能量景观，因此需要对二级结构的整个集合进行全面的表示，例如RNA二级结构的各种特征的概率分布。提出了一种有效计算任意整数标量/向量函数在二级结构上分布的一般方法。我们还展示了两个具体的算法，从参考结构的汉明距离和5 <$− 3 <$距离，这可以通过我们的一般方法来构造。这些实际应用表明了该方法的有效性。所提出的方法提供了一个清晰和全面的过程来构建各种整数特征分布的算法。此外，整数向量的分布，即不同整数分数的组合，也可以通过应用我们的二维扩展技术来描述。
Although the needs for analyses of secondary structures of RNAs are increasing, prediction of the secondary structures of RNAs are not always reliable. Because an RNA may have a complicated energy landscape, comprehensive representations of the whole ensemble of the secondary structures, such as the probability distributions of various features of RNA secondary structures are required. A general method to efficiently compute the distribution of any integer scalar/vector function on the secondary structure is proposed. We also show two concrete algorithms, for Hamming distance from a reference structure and for 5ʹ − 3ʹ distance, which can be constructed by following our general method. These practical applications of this method show the effectiveness of the proposed method. The proposed method provides a clear and comprehensive procedure to construct algorithms for distributions of various integer features. In addition, distributions of integer vectors, that is a combination of different integer scores, can be also described by applying our 2D expanding technique.