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Archaea
Volume 1, Issue 3, Pages 185-190
http://dx.doi.org/10.1155/2003/458235
Research Article

Remarkable sequence signatures in archaeal genomes

1The Center for Applied Genomics, Hospital for Sick Children, Toronto, Ontario M5G 1Z8, Canada
2Bioinformatics Supercomputing Centre, The Genomics and Genetics Biology Program, Hospital for Sick Children, Toronto, Ontario M5G 1Z8, Canada

Received 15 October 2002; Accepted 6 November 2002

Copyright © 2003 Hindawi Publishing Corporation. 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. G. Achaz, E.P. Rocha, P. Netter, and E. Coissac, “Origin and fate of repeats in bacteria,” Nucleic Acids Res., vol. 30, pp. 2987–2994, 2002. View at Google Scholar
  2. K.A. Bailey and J.N. Reeve, “DNA repeats and archaeal nucleosome positioning,” Res. Microbiol., vol. 150, pp. 701–709, 1999. View at Google Scholar
  3. K. Brugger, P. Redder, Q. She, F. Confalonieri, Y. Zivanovic, and R.A. Garrett, “Mobile elements in archaeal genomes,” FEMS Microbiol. Lett., vol. 206, pp. 131–141, 2002. View at Google Scholar
  4. S.T. Cole, P. Supply, and N. Honore, “Repetitive sequences in Mycobacterium leprae and their impact on genome plasticity,” Lepr. Rev., vol. 72, pp. 449–461, 2001. View at Google Scholar
  5. R. Cox and S.M. Mirkin, “Characteristic enrichment of DNA repeats in different genomes,” Proc. Natl. Acad. Sci. USA, vol. 94, pp. 5237–5242, 1997. View at Google Scholar
  6. P.J. Deschavanne, A. Giron, J. Vilain, G. Fagot, and B. Fertil, “Genomic signature: characterization and classification of species assessed by chaos game representation of sequences,” Mol. Biol. Evol., vol. 16, pp. 1391–1399, 1999. View at Google Scholar
  7. J. Heringa, “Detection of internal repeats: how common are they?” Curr. Opin. Struct. Biol., vol. 8, pp. 338–345, 1998. View at Google Scholar
  8. R. Jansen, J.D. Van Embden, W. Gaastra, and L.M. Schouls, “Identification of genes that are associated with DNA repeats in prokaryotes,” Mol. Microbiol., vol. 43, pp. 1565–1575, 2002. View at Google Scholar
  9. R. Jansen, J.D. Van Embden, W. Gaastra, and L.M. Schouls, “Identification of a novel family of sequence repeats among prokaryotes,” Omics, vol. 6, pp. 23–33, 2002. View at Google Scholar
  10. S. Karlin and C. Burge, “Dinucleotide relative abundance extremes: a genomic signature,” Trends Genet., vol. 11, pp. 283–290, 1995. View at Google Scholar
  11. S. Karlin and C. Burge, “Trinucleotide repeats and long homopeptides in genes and proteins associated with nervous system disease and development,” Proc. Natl. Acad. Sci. USA, vol. 93, pp. 1560–1565, 1996. View at Google Scholar
  12. T. Kawashima, Y. Yamamoto, H. Aramaki et al., “Determination of the complete genomic DNA sequence of Thermoplasma volcanium GSS1,” Proc. Jpn. Acad. Ser. B, vol. 75, pp. 213–218, 1999. View at Google Scholar
  13. S. Levy, L. Compagnoni, E.W. Myers, and G.D. Stormo, “Xlandscape: the graphical display of word frequencies in sequences,” Bioinformatics, vol. 14, pp. 74–80, 1998. View at Google Scholar
  14. K.S. Makarova, L. Aravind, Y.I. Wolf, R.L. Tatusov, K.W. Minton, E.V. Koonin, and M.J. Daly, “Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics,” Microbiol. Mol. Biol. Rev., vol. 65, pp. 44–79, 2001. View at Google Scholar
  15. N. Ogata and T. Miura, “Elongation of tandem repetitive DNA by the DNA polymerase of the hyperthermophilic archaeon Thermococcus litoralis at a hairpin–coil transitional state: a model of amplification of a primordial simple DNA sequence,” Biochemistry, vol. 39, pp. 13993–14001, 2000. View at Google Scholar
  16. G. Pesole, N. Prunella, S. Liuni, M. Attimonelli, and C. Saccone, “WORDUP: an efficient algorithm for discovering statistically significant patterns in DNA sequences,” Nucleic Acids Res., vol. 20, pp. 2871–2875, 1992. View at Google Scholar
  17. K. Quandt, K. Frech, H. Karas, E. Wingender, and T. Werner, “MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data,” Nucleic Acids Res., vol. 23, pp. 4878–4884, 1995. View at Google Scholar
  18. E.P. Rocha, A. Viari, and A. Danchin, “Oligonucleotide bias in Bacillus subtilis: general trends and taxonomic comparisons,” Nucleic Acids Res., vol. 26, pp. 2971–2980, 1998. View at Google Scholar
  19. D. Romero, J. Martinez-Salazar, E. Ortiz, C. Rodriguez, and E. Valencia-Morales, “Repeated sequences in bacterial chromosomes and plasmids: a glimpse from sequenced genomes,” Res. Microbiol., vol. 150, pp. 735–743, 1999. View at Google Scholar
  20. T.H. Tang, J.P. Bachellerie, and J.P. Bachellerie, “Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus,” Proc. Natl. Acad. Sci. USA, vol. 99, pp. 7536–7541, 2002. View at Google Scholar
  21. J. Van Helden, B. Andre, and J. Collado-Vides, “Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies,” J. Mol. Biol., vol. 281, pp. 827–842, 1998. View at Google Scholar