Several papers, in which the seven clusters pattern was described and visualized:

  1. Gorban A., Popova T., Zinovyev A. Four basic symmetry types in the universal 7-cluster structure of 143 complete bacterial genomic sequences. 2004. IHES Preprint. M/04/49.
  2. Gorban A., Zinovyev A., Popova T. Seven clusters in genomic triplet distributions. 2003. In Silico Biology. V.3, 0039.
  3. Ou HY, Guo FB, Zhang CT. Analysis of nucleotide distribution in the genome of Streptomyces coelicolor A3(2) using the Z curve method. 2003. FEBS Lett. 540(1-3):188-94.
  4. Zinovyev A., Gorban A., Popova T. Self-Organizing Approach for Automated Gene Identifcation. 2003. Open Sys.&Information Dyn. 10:1-13.
  5. Zinovyev A. Visualizing the spatial structure of triplet distributions in genetic texts. 2002. IHES Preprint. M/02/28.  
Related papers, on clusterization of genetic sequences:
  1. Audic S, Claverie JM. Self-identification of protein-coding regions in microbial genomes. Proc Natl Acad Sci U S A. 1998 Aug 18;95(17):10026-31.
  2. Baldi P. On the convergence of a clustering algorithm for protein-coding regions in microbial genomes. Bioinformatics. 2000 Apr;16(4):367-71.
Related papers, on using frequency of short words dictionaries:
  1. Sadovsky M.G. The Method to Compare Nucleotide Sequences Based on the Minimum Entropy Principle. Bulletin of Mathematical Biology, March 2003, vol. 65, iss. 2, pp. 309-322(14)
  2. Gorban AN, Bugaenko NN, Sadovsky MG. Maximum entropy method in analysis of genetic text and measurement of its information content. Open systems and information dynamics. Netherlands, 5, 1998. - pp.265-278.

Related papers, on visualization of codon usage in genomes:

  1. Carbone A., Zinovyev A., Kepes F. Codon Adaptation Index as a measure of dominating codon bias. 2003. Bioinformatics. 19, N13, p.2005-2015.
  2. Medigue, C., T. Rouxel, P. Vigier, A. Henaut and A. Danchin, (1991). Evidence for horizontal gene transfer in Escherichia coli speciation. Journal of Molecular Biology 222: 851-856.
  3. Moszer I, Rocha EP, Danchin A. Codon usage and lateral gene transfer in Bacillus subtilis.Curr Opin Microbiol. 1999 Oct;2(5):524-8.
  4. Analysis of Codon Usage Patterns of Bacterial Genomes Using the Self-Organizing Map (Huai-Chun Wang et al., Mol. Biol. Evol. 18(5):792-800. 2001)

Related papers, other:

  1. Daubin V, Lerat E, Perriere G. The source of laterally transferred genes in bacterial genomes. Genome Biol. 2003;4(9):R57
  2. Nicolas P, Bize L, Muri F, Hoebeke M, Rodolphe F, Ehrlich SD, Prum B, Bessieres P. Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models. Nucleic Acids Res. 2002 Mar 15;30(6):1418-26.
  3. Hua S, Sun Z. Support vector machine approach for protein subcellular localization prediction. Bioinformatics. 2001 Aug;17(8):721-8.
  4. Fuglsang A. Codon optimizer: a freeware tool for codon optimization. Protein Expr Purif. 2003 Oct;31(2):247-9.
  1. Codon usage database
  2. Z-curve highGC