FAST ALGORITHM FOR PREDICTING THE SECONDARY STRUCTURE OF SINGLE-STRANDED RNA
FAST ALGORITHM FOR PREDICTING THE SECONDARY STRUCTURE OF SINGLE-STRANDED RNA
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预测单链 RNA 二级结构的快速算法
DOI：
10.1073/pnas.77.11.6309
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发表时间：
1980-01-01
期刊：
影响因子：
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通讯作者：
JACOBSON, AB
中科院分区：
文献类型：
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作者：
NUSSINOV, R;JACOBSON, AB
提出了一种寻找长单链RNA最稳定二级结构的计算机方法。它比现有代码快1-2个数量级。对于N个核苷酸长的链，其应用所需的时间随着N3而增加。在一次运行中可以搜索多达1000个核苷酸。该方法是系统的，并建立一个最佳的结构，在一个简单的归纳过程的基础上，一个精确的数学算法。构造了两个简单的半矩阵，并通过简单的回溯过程直接从第二个矩阵中读取最佳折叠形式。该程序利用已公布的碱基配对能量值来计算具有最低自由能的1结构。
A computer method is presented for finding the most stable secondary structures in long single-stranded RNAs. It is 1-2 orders of magnitude faster than existing codes. The time required for its application increases as N3 for a chain N nucleotides long. As many as 1000 nucleotides can be searched in a single run. The approach is systematic and builds an optimal structure in a straightforward inductive procedure based on an exact mathematical algorithm. Two simple half-matrices are constructed and the best folded form is read directly from the 2nd matrix by a simple back-tracking procedure. The program utilizes published values for base-pairing energies to compute 1 structure with the lowest free energy.