SOME SIMPLE COMPUTATIONAL METHODS TO IMPROVE THE FOLDING OF LARGE RNAS
SOME SIMPLE COMPUTATIONAL METHODS TO IMPROVE THE FOLDING OF LARGE RNAS
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DOI：
10.1093/nar/12.1part1.45
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发表时间：
1984-01-01
影响因子：
14.9
通讯作者：
ZUKER, M
中科院分区：
文献类型：
--
作者：
JACOBSON, AB;GOOD, L;ZUKER, M
描述了提高 Zuker 和 Stiegler 描述的 RNA 折叠算法效率的计算方法。位寻址已用于将存储器需求从 2NxN 减少到 NxN/2。内部检查核苷酸序列的顺序已经改变，并且引入了一些携带临时信息的附加短阵列。这些变化优化了算法生成的大数据数组的管理。这些方法是为与 UNIVAC 1100/82 计算机一起使用而开发的。然而，它们很容易适应研究论文计算机。尤其是那些具有虚拟内存功能的。对长达 1000 个核苷酸的序列的分析相对常规，并且更大的搜索也是可行的。还讨论了该算法的一些局限性和应用。
Computational methods are described which increase the efficiency of the RNA folding algorthm described by Zuker and Stiegler. Bit addressing has been used to reduce the memory requirements from 2NxN to NxN/2. The order in which the nucleotide sequence is examined internally has been altered, and some additional short arrays which carry temporary information have been introduced. These changes optimize the management of the large data arrays generated by the algorithm. The methods were developed for use with a UNIVAC 1100/82 computer. They are, however, easily adaptable to research-article computers; especially those with virtual memory capabilities. The analysis of sequences up to 1000 nucleotides long are relatively routine, and larger searches are also feasible. Some limitations and applications of the algorithm are also discussed.