Visualization of microorganism classification on power spectrums of complete DNA sequences using clustering analysis and multidimensional scaling

  • Authors:

  • Cheng-Chang Jeng;I-Ching Yang;Ting-Jia Lain;Kun-Lin Hsieh;Chun-Nan Lin

  • Affiliations:

  • Systematic and Theoretical Science Research Group, National Taitung University, Taitung, Taiwan;Systematic and Theoretical Science Research Group, National Taitung University, Taitung, Taiwan;Systematic and Theoretical Science Research Group, National Taitung University, Taitung, Taiwan;Systematic and Theoretical Science Research Group, National Taitung University, Taitung, Taiwan;Department of Management Information System, National Chung Cheng University, Chia-Yi, Taiwan

  • Venue:
  • ICCOMP'06 Proceedings of the 10th WSEAS international conference on Computers
  • Year:
  • 2006

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Abstract

The coding structure of nucleotide sequences can be investigated and visually observe via power spectrums obtained by applying Fourier transforms to complete DNA sequences. The proposed method also provides dimension reduction for complete DNA sequences. To construct tree-like diagram, which looks like a taxonomy tree, hierarchical cluster analysis (HCA) was applied to transformed DNA sequences. Also, multidimensional scaling (MDS) was utilized to help visually investigate relationships among microorganisms in a low-dimensional space. The combination of the analysis of power spectrums on complete DNA sequences with HCA and MDS is suggested to examine coding structure and clustering of 15 microorganisms, which consists of some members of Escherichia coli, Pyrococcus, and Bacillus genera. The results of clustering and perceptual map from the combined mathematical model correspond with the recent findings found by others. Especially note that, with the proposed method, Pyrococcus furiosus is not within the lineage of Pyrococcus abyssi and Pyrococcus horikoshii, and also Bacillus halodurans C-125 is not within the lineage of Bacillus cereus genus that consists of Bacillus anthracis and Bacillus cereus family. In conclusion, the results constructed by HCA and MDS on the power spectrums of complete DNA sequences provide biologists mathematical tools to verify the taxonomy of microorganism and speed up analytic process.