A structural similarity analysis of double-helical DNA
A structural similarity analysis of double-helical DNA
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DOI：
10.1016/j.jmb.2004.08.092
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发表时间：
2004-10-29
影响因子：
5.6
通讯作者：
Willett, P
中科院分区：
文献类型：
--
作者：
Gardiner, EJ;Hunter, CA;Willett, P
计算了所有32,896个独特DNA八聚体序列的结构特性数据库，包括稳定性，最小能量构象和灵活性的信息。数据库的内容已经使用各种欧氏距离相似度量进行了分析。序列相似度与结构相似度的全局比较表明，DNA的结构特性比序列的多样性要小得多，DNA序列空间比DNA结构空间更大、更多样化。因此，有许多非常不同的序列具有非常相似的结构特性，这可能有助于识别具有相似功能特性的DNA基序，而这些功能特性在序列中并不明显。另一方面，也有少数几乎相同的序列具有非常不同的结构特性，这可能会在用于基于序列比对识别功能的方法中产生假阳性。一个简单的验证测试表明，结构相似性可以区分启动子和非启动子DNA。结合结构和序列相似性可以提高启动子的召回率，这比单独使用任何一种相似性测量都要高，这表明双螺旋DNA结构中确实存在从序列中不易明显得到的信息。(C) 2004 Elsevier Ltd.版权所有。
A database of the structural properties of all 32,896 unique DNA octamer sequences has been calculated, including information on stability, the minimum energy conformation and flexibility. The contents of the database have been analysed using a variety of Euclidean distance similarity measures. A global comparison of sequence similarity with structural similarity shows that the structural properties of DNA are much less diverse than the sequences, and that DNA sequence space is larger and more diverse than DNA structure space. Thus, there are many very different sequences that have very similar structural properties, and this may be useful for identifying DNA motifs that have similar functional properties that are not apparent from the sequences. On the other hand, there are also small numbers of almost identical sequences that have very different structural properties, and these could give rise to false-positives in methods used to identify function based on sequence alignment. A simple validation test demonstrates that structural similarity can differentiate between promoter and non-promoter DNA. Combining structural and sequence similarity improves promoter recall beyond that possible using either similarity measure alone, demonstrating that there is indeed information available in the structure of double-helical DNA that is not readily apparent from the sequence. (C) 2004 Elsevier Ltd. All rights reserved.