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BioMed Research International
Volume 2014, Article ID 765648, 11 pages
http://dx.doi.org/10.1155/2014/765648
Research Article

A Novel Bioinformatics Method for Efficient Knowledge Discovery by BLSOM from Big Genomic Sequence Data

1Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma-shi, Nara 630-0192, Japan
2Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Shiga-ken 526-0829, Japan
3Sino-Dutch Biomedical and Information Engineering School, Northeastern University, Shenyang, Liaoning 110004, China

Received 24 October 2013; Accepted 14 February 2014; Published 3 April 2014

Academic Editor: Md. Altaf-Ul-Amin

Copyright © 2014 Yu Bai et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. R. Nussinov, “Doublet frequencies in evolutionary distinct groups,” Nucleic Acids Research, vol. 12, no. 3, pp. 1749–1763, 1984. View at Publisher · View at Google Scholar · View at Scopus
  2. G. J. Phillips, J. Arnold, and R. Ivarie, “Mono-through hexanucleotide composition of the Escherichia coli genome: a markov chain analysis,” Nucleic Acids Research, vol. 15, no. 6, pp. 2611–2626, 1987. View at Publisher · View at Google Scholar · View at Scopus
  3. S. Karlin, “Global dinucleotide signatures and analysis of genomic heterogeneity,” Current Opinion in Microbiology, vol. 1, no. 5, pp. 598–610, 1998. View at Google Scholar · View at Scopus
  4. S. Karlin, A. M. Campbell, and J. Mrázek, “Comparative DNA analysis across diverse genomes,” Annual Review of Genetics, vol. 32, pp. 185–225, 1998. View at Publisher · View at Google Scholar · View at Scopus
  5. E. P. C. Rocha, A. Viari, and A. Danchin, “Oligonucleotide bias in Bacillus subtilis: general trends and taxonomic comparisons,” Nucleic Acids Research, vol. 26, no. 12, pp. 2971–2980, 1998. View at Publisher · View at Google Scholar · View at Scopus
  6. A. J. Gentles and S. Karlin, “Genome-scale compositional comparisons in eukaryotes,” Genome Research, vol. 11, no. 4, pp. 540–546, 2001. View at Publisher · View at Google Scholar · View at Scopus
  7. G. Bernardi, Structural and Evolutionary Genomics: Natural Selection in Genome Evolution, Elsevier, New York, NY, USA, 2004.
  8. S. Vinga and J. Almeida, “Alignment-free sequence comparison: a review,” Bioinformatics, vol. 19, no. 4, pp. 513–523, 2003. View at Publisher · View at Google Scholar · View at Scopus
  9. A. Bolshoy, “DNA sequence analysis linguistic tools: contrast vocabularies, compositional spectra and linguistic complexity,” Appl Bioinformatics, vol. 2, no. 2, pp. 103–112, 2003. View at Google Scholar · View at Scopus
  10. T. Kohonen, “Self-organized formation of topologically correct feature maps,” Biological Cybernetics, vol. 43, no. 1, pp. 59–69, 1982. View at Google Scholar · View at Scopus
  11. T. Kohonen, “The self-organizing map,” Proceedings of the IEEE, vol. 78, no. 9, pp. 1464–1480, 1990. View at Publisher · View at Google Scholar · View at Scopus
  12. T. Kohonen, E. Oja, O. Simula, A. Visa, and J. Kangas, “Engineering applications of the self-organizing map,” Proceedings of the IEEE, vol. 84, no. 10, pp. 1358–1384, 1996. View at Publisher · View at Google Scholar · View at Scopus
  13. S. Kanaya, Y. Kudo, T. Abe, T. Okazaki, D. C. Carlos, and T. Ikemura, “Gene classification by self-organization mapping of codon usage in bacteria with completely sequenced genome,” Genome Informatics Series. Workshop on Genome Informatics, vol. 13, pp. 369–371, 1998. View at Google Scholar
  14. T. Abe, S. Kanaya, M. Kinouchi, Y. Ichiba, T. Kozuki, and T. Ikemura, “A novel bioinformatic strategy for unveiling hidden genome signatures of eukaryotes: self-organizing map of oligonucleotide frequency,” Genome Informatics Series. Workshop on Genome Informatics, vol. 13, pp. 12–20, 2002. View at Google Scholar · View at Scopus
  15. T. Abe, S. Kanaya, M. Kinouchi, Y. Ichiba, T. Kozuki, and T. Ikemura, “Informatics for unveiling hidden genome signatures,” Genome Research, vol. 13, no. 4, pp. 693–702, 2003. View at Publisher · View at Google Scholar · View at Scopus
  16. T. Abe, H. Sugawara, S. Kanaya, and T. Ikemura, “Sequences from almost all prokaryotic, eukaryotic, and viral genomes available could be classified according to genomes on a large-scale Self-Organizing Map constructed with the Earth Simulator,” Journal of the Earth Simulator, vol. 6, pp. 17–23, 2006. View at Google Scholar
  17. Y. Iwasaki, K. Wada, Y. Wada, T. Abe, and T. Ikemura, “Notable clustering of transcription-factor-binding motifs in human pericentric regions and its biological significance,” Chromosome Research, vol. 21, pp. 461–474, 2013. View at Google Scholar
  18. T. Abe, S. Kanaya, H. Uehara, and T. Ikemura, “A novel bioinformatics strategy for function prediction of poorly-characterized protein genes obtained from metagenome analyses,” DNA Research, vol. 16, no. 5, pp. 287–298, 2009. View at Publisher · View at Google Scholar · View at Scopus
  19. A. Ultsch, “Self organized feature maps for monitoring and knowledge acquisition of a chemical process,” in Proceedings of the International Conference on Artificial Neural Networks (ICANN '93), S. Gielen and B. Kappen, Eds., pp. 864–867, Springer, London, UK, 1993. View at Google Scholar
  20. G. Bernardi, B. Olofsson, and J. Filipski, “The mosaic genome of warm-blooded vertebrates,” Science, vol. 228, no. 4702, pp. 953–958, 1985. View at Google Scholar · View at Scopus
  21. T. Ikemura, “Codon usage and tRNA content in unicellular and multicellular organisms,” Molecular Biology and Evolution, vol. 2, no. 1, pp. 13–34, 1985. View at Google Scholar · View at Scopus
  22. T. Ikemura and S. Aota, “Global variation in G + C content along vertebrate genome DNA. Possible correlation with chromosome band structures,” Journal of Molecular Biology, vol. 203, no. 1, pp. 1–13, 1988. View at Google Scholar · View at Scopus
  23. T. Ikemura and K.-N. Wada, “Evident diversity of codon usage patterns of human genes with respect to chromosome banding patterns and chromosome numbers; relation between nucleotide sequence data and cytogenetic data,” Nucleic Acids Research, vol. 19, no. 16, pp. 4333–4339, 1991. View at Google Scholar · View at Scopus
  24. C. Maison, D. Bailly, A. H. F. M. Peters et al., “Higher-order structure in pericentric heterochromatin involves a distinct pattern of histone modification and an RNA component,” Nature Genetics, vol. 30, no. 3, pp. 329–334, 2002. View at Publisher · View at Google Scholar · View at Scopus
  25. C. Maison and G. Almouzni, “HP1 and the dynamics of heterochromatin maintenance,” Nature Reviews Molecular Cell Biology, vol. 5, no. 4, pp. 296–304, 2004. View at Publisher · View at Google Scholar · View at Scopus
  26. A. V. Probst, E. Dunleavy, and G. Almouzni, “Epigenetic inheritance during the cell cycle,” Nature Reviews Molecular Cell Biology, vol. 10, no. 3, pp. 192–206, 2009. View at Publisher · View at Google Scholar · View at Scopus
  27. A. V. Probst, I. Okamoto, M. Casanova, F. El Marjou, P. le Baccon, and G. Almouzni, “A Strand-specific burst in transcription of pericentric satellites is required for chromocenter formation and early mouse development,” Developmental Cell, vol. 19, no. 4, pp. 625–638, 2010. View at Publisher · View at Google Scholar · View at Scopus
  28. A. V. Probst and G. Almouzni, “Heterochromatin establishment in the context of genome-wide epigenetic reprogramming,” Trends in Genetics, vol. 27, no. 5, pp. 177–185, 2011. View at Publisher · View at Google Scholar · View at Scopus
  29. T. Fukagawa, M. Nogami, M. Yoshikawa et al., “Dicer is essential for formation of the heterochromatin structure in vertebrate cells,” Nature Cell Biology, vol. 6, no. 8, pp. 784–791, 2004. View at Publisher · View at Google Scholar · View at Scopus
  30. C. Maison, D. Bailly, D. Roche et al., “SUMOylation promotes de novo targeting of HP1 ± to pericentric heterochromatin,” Nature Genetics, vol. 43, no. 3, pp. 220–227, 2011. View at Publisher · View at Google Scholar · View at Scopus
  31. Y. Du, C. N. Topp, and R. K. Dawe, “DNA binding of centromere protein C (CENPC) is stabilized by single-stranded RNA,” PLoS Genetics, vol. 6, no. 2, Article ID e1000835, 2010. View at Publisher · View at Google Scholar · View at Scopus
  32. L. H. Wong, K. H. Brettingham-Moore, L. Chan et al., “Centromere RNA is a key component for the assembly of nucleoproteins at the nucleolus and centromere,” Genome Research, vol. 17, no. 8, pp. 1146–1160, 2007. View at Publisher · View at Google Scholar · View at Scopus
  33. R. I. Amann, W. Ludwig, and K.-H. Schleifer, “Phylogenetic identification and in situ detection of individual microbial cells without cultivation,” Microbiological Reviews, vol. 59, no. 1, pp. 143–169, 1995. View at Google Scholar · View at Scopus
  34. P. Hugenholtz and N. R. Pace, “Identifying microbial diversity in the natural environment: a molecular phylogenetic approach,” Trends in Biotechnology, vol. 14, no. 6, pp. 190–197, 1996. View at Publisher · View at Google Scholar · View at Scopus
  35. M. R. Rondon, P. R. August, A. D. Bettermann et al., “Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms,” Applied and Environmental Microbiology, vol. 66, no. 6, pp. 2541–2547, 2000. View at Publisher · View at Google Scholar · View at Scopus
  36. P. Lorenz, K. Liebeton, F. Niehaus, and J. Eck, “Screening for novel enzymes for biocatalytic processes: accessing the metagenome as a resource of novel functional sequence space,” Current Opinion in Biotechnology, vol. 13, no. 6, pp. 572–577, 2002. View at Publisher · View at Google Scholar · View at Scopus
  37. E. F. DeLong, “Microbial population genomics and ecology,” Current Opinion in Microbiology, vol. 5, no. 5, pp. 520–524, 2002. View at Publisher · View at Google Scholar · View at Scopus
  38. P. D. Schloss and J. Handelsman, “Biotechnological prospects from metagenomics,” Current Opinion in Biotechnology, vol. 14, no. 3, pp. 303–310, 2003. View at Publisher · View at Google Scholar · View at Scopus
  39. T. Abe, H. Sugawara, M. Kinouchi, S. Kanaya, and T. Ikemura, “Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples,” DNA Research, vol. 12, no. 5, pp. 281–290, 2005. View at Publisher · View at Google Scholar · View at Scopus
  40. H. Hayashi, T. Abe, M. Sakamoto et al., “Direct cloning of genes encoding novel xylanases from the human gut,” Canadian Journal of Microbiology, vol. 51, no. 3, pp. 251–259, 2005. View at Publisher · View at Google Scholar · View at Scopus
  41. R. Nakao, T. Abe, A. M. Nijhof et al., “A novel approach, based on BLSOMs (Batch Learning Self-Organizing Maps), to the microbiome analysis of ticks,” The ISME Journal, vol. 7, pp. 1003–1015, 2013. View at Google Scholar
  42. H. Uehara, Y. Iwasaki, C. Wada, T. Ikemura, and T. Abe, “A novel bioinformatics strategy for searchingindustrially useful genome resources frommetagenomic sequence libraries,” Genes and Genetic Systems, vol. 86, no. 1, pp. 53–66, 2011. View at Publisher · View at Google Scholar · View at Scopus