The study of applying a systematic procedure based on SOFM clustering technique into organism clustering

Expert Systems with Applications

Volumn 33, Issue 2, 2007, Pages 330-336

  Hsieh, Kun Lin ^a   Jeng, Cheng Chang ^a   Yang, I Ching ^a   Chen, Yan Kwang ^b   Lin, Chun Nan ^c  

^a NATIONAL TAITUNG UNIVERSITY   (Taiwan)

^b NATIONAL TAICHUNG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Taiwan)

^c NATIONAL CHUNG CHENG UNIVERSITY   (Taiwan)

Author keywords

Clustering analysis; DNA sequence; Organism classification; Self organizing feature mapping (SOFM)

Indexed keywords

DNA SEQUENCES; EXPERT SYSTEMS; INFORMATION RETRIEVAL; MOLECULAR STRUCTURE;

BIOLOGICAL ORGANISMS; CLUSTERING ANALYSIS; ORGANISM CLASSIFICATION; SELF-ORGANIZING FEATURE MAPPING (SOFM);

MICROORGANISMS;

EID: 33846511783     PISSN: 09574174     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.eswa.2006.05.032     Document Type: Article

References (19)

1. Chen Y.H., Nyeo S.L., and Yu J.P. Power-laws in the complete sequences of human genome. Journal of Biological Systems 13 (2005) 105-115
2. De Sousa Vieira M. Statistics of DNA sequences: A low-frequency analysis. Physical Review E 60 (1999) 5932-5937
3. Doolittle R.F., Feng D.-F., Tsang S., Cho G., and Little E. Determining divergence times of the major Kingdoms of living organisms with a protein clock. Science 271 (1996) 470-477
4. Fukushima A., Ikemura T., Kinouchi M., Oshima T., Kudo Y., Mori H., et al. Periodicity in prokaryotic and eukaryotic genomes identified by power spectrum analysis. Gene 300 (2002) 203-211
5. Haykin S. Neural networks: A comprehensive foundation (1994), Macmillan College Publishing Company, New York
6. Helgason E., Økstad D.A., Caugant D.A., Johansen G.A., Fouet A., Mock M., et al. Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis-one species on the basis of genetic evidence. Applied and Environmental Microbiology 66 6 (2000) 2627-2630
7. Herzel H., and Grosse I. Measuring correlations in symbolic sequences. Physica A 216 (1995) 518-542
8. Herzel H., Weiss O., and Trifonov E.N. 10-11 bp periodicities in complete genome reflect protein structure and DNA folding. Bioinformatics 15 (1999) 187-193
9. Hinton G.E. Connectionist learning procedures. Artificial Intelligence 40 (1989) 185-234
10. Isohata Y., and Hayashi M. Analyses of DNA base sequences for eukaryotes in terms of power spectrum method. Japanese Journal of Applied Physics 44 (2005) 1143-1146
11. Kohonen T. Self-organized formation of topologically correct feature maps. Biological Cybernetics 43 (1982) 59-69
12. Kohonen T. The self-organizing map. Proceedings of the IEEE 78 (1990) 1464-1480
13. Lee W.J., and Luo L.F. Periodicity of base correlation in nucleotide sequence. Physical Review E 56 (1997) 848-851
14. Lippmann R.P. An introduction to computing with neural nets. IEEE Communications Magazine 27 (1987) 47-64
15. Nyeo S.L., Yang I.C., and Wu C.H. Spectral classification of archaeal and bacterial genomes. Journal of Biological Systems 10 (2002) 233-241
16. Odile L., Raymond R., Valerie P.B., Simone D., Roland H., Jacques D., et al. Genome Evolution at the genus level: Comparison of three complete genomes of hyperthermophilic archaea. Genome Research 11 (2001) 981-993
17. Rey M.W., Ramaiya P., Nelson B.A., Brody-Karpin S.D., Zaretsky E.J., Tang M., et al. Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species. Genome Biology 5 10 (2004) R77
18. Ritter H., and Kohonen T. Self-organizing semantic maps. Biological Cybernetics 61 (1989) 241-254
19. The Institute for Genomic Research (TIGR) (2005). Genome pages. Available from http://www.tigr.org/tigr-scripts/CMR2/GenomePage3.spl?database=ntec02.