在HIV和SIV序列中检测异常RNA折叠区域。

Detection of unusual RNA folding regions in HIV and SIV sequences.

作者信息

Le S Y, Chen J H, Maizel J V

机构信息

Institute for Biological Sciences, National Research Council of Canada, Ottawa.

出版信息

Comput Appl Biosci. 1991 Jan;7(1):51-5. doi: 10.1093/bioinformatics/7.1.51.

DOI:10.1093/bioinformatics/7.1.51

Abstract

We have developed a method for detecting more stable and significant folding regions relative to others in the sequence. The algorithm is based on the calculation of the lowest free energy of RNA secondary structures and Monte Carlo simulation. For any given RNA segment, the stability and statistical significance of RNA folding are assessed by two measures: the stability score and the significance score. The stability score measures the degree of thermodynamic stability of the segment between all possible biological segments in the RNA sequence. The significance score characterizes the specific arrangement of the nucleotides in the segment that could imply a structural role for the sequence information. Using these two measures, we are able to detect a series of distinct folding regions where highly stable and statistically significant secondary structures occur in human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) sequences.

摘要

我们已经开发出一种方法，用于检测序列中相对于其他区域更稳定且更显著的折叠区域。该算法基于RNA二级结构最低自由能的计算以及蒙特卡罗模拟。对于任何给定的RNA片段，RNA折叠的稳定性和统计学显著性通过两种度量来评估：稳定性得分和显著性得分。稳定性得分衡量RNA序列中所有可能的生物学片段之间该片段的热力学稳定程度。显著性得分表征该片段中核苷酸的特定排列，这可能意味着序列信息具有结构作用。使用这两种度量，我们能够在人类免疫缺陷病毒（HIV）和猴免疫缺陷病毒（SIV）序列中检测到一系列不同的折叠区域，其中会出现高度稳定且具有统计学显著性的二级结构。

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