一种寻找一组能量最优RNA二级结构的新方法。
A new method to find a set of energetically optimal RNA secondary structures.
作者信息
Benedetti G, De Santis P, Morosetti S
机构信息
Department of Chemistry, University of Rome, Italy.
出版信息
Nucleic Acids Res. 1989 Jul 11;17(13):5149-61. doi: 10.1093/nar/17.13.5149.
We present a computer method to determine nucleic acid secondary structures. It is based on three steps: 1) the search for all possible helical regions relied on a mathematical approach derived from the convolution theorem; it uses a tetradimensional complex vector representation of the bases along the sequence; 2) a 'tree' search for a set of minimum free energy structures, by the aid of an approximate energy evaluation to reduce the computer time requirements; 3) the exact calculation and refinement of the energies. A method to introduce the experimental data and reach an arrangement between them and the free energy minimization criterion is shown. In order to demonstrate the confidence of the program a test on four RNA sequences is performed. The method has computer time requirement proportional to N2, where N is the length of the sequence and retrieves a set of optimal free energy structures.
我们提出了一种确定核酸二级结构的计算机方法。它基于三个步骤：1）通过源自卷积定理的数学方法搜索所有可能的螺旋区域；它使用沿着序列的碱基的四维复向量表示；2）借助近似能量评估进行“树形”搜索以找到一组最小自由能结构，从而减少计算机时间需求；3）对能量进行精确计算和细化。展示了一种引入实验数据并使其与自由能最小化标准达成协调的方法。为了证明该程序的可靠性，对四个RNA序列进行了测试。该方法的计算机时间需求与N²成正比，其中N是序列的长度，并且能检索出一组最优自由能结构。
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