利用序列比较来检测tRNA基因中的“一致性”。
The use of sequence comparison to detect 'identities' in tRNA genes.
作者信息
Sagara J I, Shimizu S, Kawabata T, Nakamura S, Ikeguchi M, Shimizu K
机构信息
Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113, Japan.
出版信息
Nucleic Acids Res. 1998 Apr 15;26(8):1974-9. doi: 10.1093/nar/26.8.1974.
We have developed a computational method that detects 'identities' in tRNA genes by using principal component analysis to classify the sequences of bases in tRNA genes into groups of similar sequences and then comparing the distribution of sequences of bases, in order to extract characteristic bases that are conserved within a group but differ between groups. These classification and comparison procedures are applied recursively to classify the sequences into hierarchical groups, so that multiple levels of characteristic sites can be detected. By using this computational method, we were able to detect many characteristic sites in the T and D domains of tRNAs, as well as the characteristic sites that had already been detected experimentally. This suggests that bases not only in the contact regions but also in the elbow regions, which determine the structure and dynamics of the whole tRNA molecule, are important to the tRNA-aminoacyl tRNA synthetase recognition.
我们开发了一种计算方法，该方法通过主成分分析将tRNA基因中的碱基序列分类为相似序列组，然后比较碱基序列的分布，来检测tRNA基因中的“特征”，以便提取在组内保守但在组间不同的特征碱基。这些分类和比较程序被递归应用，将序列分类为层次组，从而可以检测到多个层次的特征位点。通过使用这种计算方法，我们能够在tRNA的T和D结构域中检测到许多特征位点，以及已经通过实验检测到的特征位点。这表明，不仅在接触区域，而且在决定整个tRNA分子结构和动态的肘部区域的碱基，对于tRNA-氨酰tRNA合成酶识别都很重要。
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