Analysis of Aspergillus oryzae tRNA Genes Using Multivariate Analysis

The method uses the principal component analysis and multidimensional scaling method to classify the sequences of tRNA genes into multiple groups of similar sequences, and also to extract characteristic bases that are conserved within a group but differ from other groups. This procedure was applied recursively to classify the sequences into hierarchical groups so that characteristic sites can be detected more precisely. The advantages of our method are as follows; (1)it allows comparison of the whole sequence; (2)Gene sequences are represented as vectors in a generalized sequence space; (3)the bases of each sequence are projected individually onto the same sequence space. We applied our method to the sequences of tRNA genes from Aspergillus oryzae which is used extensively for the production of the traditional Japanese fermented foods and detected not only that bases that are always conserved but also bases that are often conserved.