一些改善大型RNA折叠的简单计算方法。
Some simple computational methods to improve the folding of large RNAs.
作者信息
Jacobson A B, Good L, Simonetti J, Zuker M
出版信息
Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):45-52. doi: 10.1093/nar/12.1part1.45.
Abstract
Computational methods are described which increase the efficiency of the RNA folding algorithm 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 other 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.
摘要
本文描述了一些计算方法，这些方法提高了祖克（Zuker）和施蒂格勒（Stiegler）所描述的RNA折叠算法的效率。采用位寻址方式将内存需求从2NxN减少到NxN/2。内部检查核苷酸序列的顺序已被改变，并且引入了一些携带临时信息的额外短数组。这些变化优化了该算法生成的大数据数组的管理。这些方法是为与UNIVAC 1100/82计算机配合使用而开发的。然而，它们很容易适用于其他计算机，尤其是那些具有虚拟内存功能的计算机。对长度达1000个核苷酸的序列进行分析相对常规，更大规模的搜索也是可行的。本文还讨论了该算法的一些局限性和应用。
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