Lück R, Steger G, Riesner D
Institut für Physikalische Biologie, Heinrich-Heine-Universität, Düsseldorf, FRG.
J Mol Biol. 1996 May 24;258(5):813-26. doi: 10.1006/jmbi.1996.0289.
An algorithm for prediction of conserved secondary structure of single-stranded RNA is presented. For each RNA of a set of homologous RNAs optimal and suboptimal secondary structures are calculated and stored in a base-pair probability matrix. A multiple sequence alignment is performed for the set of RNAs. The resulting gaps are introduced into the individual probability matrices. These homologous probability matrices are summed to give a consensus probability matrix emphasizing the conserved secondary structure elements of the RNA set. Thus the algorithm combines the advantages of thermodynamic structure prediction by energy minimization with the information obtained from phylogenetic alignment of sequences. The algorithm is applied to three examples. The REV-responsive element of HIV, the structure of which is well known from the literature, was chosen to test the algorithm. The second example is the 3' terminal segment of genomic single-stranded RNAs of cucumber mosaic viruses; a structure similar to that of the related brome mosaic virus was expected and was confirmed. The third example is the prion-protein mRNA from different organisms; the structure of this mRNA is not known. By application of the algorithm highly conserved hairpins were found in the prion-protein mRNA.
本文提出了一种预测单链RNA保守二级结构的算法。对于一组同源RNA中的每个RNA，计算其最优和次优二级结构，并存储在碱基对概率矩阵中。对这组RNA进行多序列比对。将比对产生的空位引入到各个概率矩阵中。将这些同源概率矩阵相加，得到一个共识概率矩阵，突出显示该RNA集合中保守的二级结构元件。因此，该算法结合了通过能量最小化进行热力学结构预测的优点以及从序列系统发育比对中获得的信息。该算法应用于三个实例。选择了HIV的REV反应元件，其结构在文献中已有详细记载，用于测试该算法。第二个实例是黄瓜花叶病毒基因组单链RNA的3'末端片段；预期其结构与相关的雀麦花叶病毒相似，并得到了证实。第三个实例是来自不同生物体的朊病毒蛋白mRNA；该mRNA的结构尚不清楚。通过应用该算法，在朊病毒蛋白mRNA中发现了高度保守的发夹结构。
