Advertisement

Molecular Biology

, Volume 35, Issue 6, pp 841–848 | Cite as

Algorithm of Regulatory Signal Recognition in DNA Sequences

  • L. V. Danilova
  • K. Yu. Gorbunov
  • M. S. Gelfand
  • V. A. Lyubetskii
Article
  • 21 Downloads

Abstract

An algorithm is proposed for extracting regulatory signals from DNA sequences. The algorithm complexity is nearly quadratic. The results of testing the algorithm on artificial and natural sequences are presented.

molecular biology regulatory signal computer logic graph algorithms 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Spellman, P.T. et al., Mol. Biol. Cell, 1998, vol. 9, pp. 3273–3297.PubMedGoogle Scholar
  2. 2.
    Roth, F.R. et al., Nature Biotechnol., 1998, vol. 16, pp. 939–945.Google Scholar
  3. 3.
    Bassett, D.E. Jr. et al., Nature Genet., 1999, vol. 21, pp. 51–55.PubMedGoogle Scholar
  4. 4.
    Bucher, P., Curr. Opin. Struct. Biol., 1999, vol. 9, pp. 400–407.PubMedGoogle Scholar
  5. 5.
    Gelfand, M.S., Koonin, E.V., and Mironov, A.A., Nucleic Acids Res., 2000, vol. 28, pp. 695–705.PubMedGoogle Scholar
  6. 6.
    McGuire, A.M., Hughes, J.D., and Church, G.M., Genome Res., 2000, vol. 10, pp. 744–757.PubMedGoogle Scholar
  7. 7.
    Gelfand, M.S., Res. Microbiol., 1999, vol. 150, pp. 755–771.PubMedGoogle Scholar
  8. 8.
    Gelfand, M.S., J. Comput. Biol., 1995, vol. 2, pp. 87–115.PubMedGoogle Scholar
  9. 9.
    Frech, K., Quandt, K., and Werner, T., Comput. Appl. Biosci., 1997, vol. 13, pp. 89–97.PubMedGoogle Scholar
  10. 10.
    Duret, L. and Bucher, P., Curr. Opin. Struct. Biol., 1997, vol. 7, pp. 399–406.PubMedGoogle Scholar
  11. 11.
    Fickett, J.W. and Wasserman, W.W., Curr. Opin. Biotechnol., 2000, vol. 11, pp. 19–24.PubMedGoogle Scholar
  12. 12.
    Stormo, G.D. and Hartzell, G.W. III., Proc. Natl. Acad. Sci. USA, 1989, vol. 86, pp. 1183–1187.PubMedGoogle Scholar
  13. 13.
    Hertz, G.Z., Hartzell, G.W. III, and Stormo, G.D., Comput. Appl. Biosci., 1990, vol. 6, pp. 81–92.PubMedGoogle Scholar
  14. 14.
    Lawrence, C.E. and Reilly, A.A., PROTEINS: Structure, Function, Genetics, 1990, vol. 7, pp. 41–51.Google Scholar
  15. 15.
    Cardon, L.R. and Stormo, G.D., J. Mol. Biol., 1992, vol. 223, pp. 159–170.PubMedGoogle Scholar
  16. 16.
    Frishman, D., Mironov, A., Gelfand, M., Gene, 1999, vol. 234, pp. 257–265.PubMedGoogle Scholar
  17. 17.
    Gelfand, M.S., Koonin, E.V., and Mironov, A.A., Nucleic Acids Res., 2000, vol. 28, pp. 695–705.PubMedGoogle Scholar
  18. 18.
    Hu, Y.-J., Sandmeyer, S., McLaughlin, C., and Kibler, D., Bioinformatics, 2000, vol. 16, pp. 222–232.PubMedGoogle Scholar
  19. 19.
    Bailey, T.L. and Elkan, C.P., Proc. 2nd Int. Conf. on Intelligent Systems for Molecular Biology ISMB'1994, 1994, pp. 28–36.Google Scholar
  20. 20.
    Bailey, T.L. and Elkan, C.P., Proc. 3rd Int. Conf. on Intelligent Sysems for Molecular Biology ISMB'1995, 1995, pp. 21–29.Google Scholar
  21. 21.
    Grundy, W.N., Bailey, T.L., and Elkan, C.P., Comput. Appl. Biosci., 1996, vol. 12, pp. 303–310.PubMedGoogle Scholar
  22. 22.
    Lukashin, A.V., Engelbrecht, J., and Brunak, S., Nucleic Acids Res., 1992, vol. 20, pp. 2511–2516.PubMedGoogle Scholar
  23. 23.
    Lawrence, C.E., Altschul, S.F., Boguski, M.S., et al., Science, 1993, vol. 262, pp. 208–214.PubMedGoogle Scholar
  24. 24.
    Roth, F.P., Hughes, D., Estep, P.W., and Church, G.M., Nature Biotech., 1998, vol. 16, pp. 939–945.Google Scholar
  25. 25.
    Frech, K., Herrmann, G., and Werner, T., Nuceic. Acids Res., 1993, vol. 21, pp. 1655–1664.Google Scholar
  26. 26.
    Quandt, K., Frech, K., Karas, H., et al., Nucleic Acids Res., 1995, vol. 23, pp. 4878–4884.PubMedGoogle Scholar
  27. 27.
    Kielbasa, Sz.M., Korbel, J.O., Beule D., et al., '2000, 2000, pp. 55–62.Google Scholar
  28. 28.
    Pesole, G., Prunella, N., Liuni S., et al., Nucleic Acids Res., 1992, vol. 20, pp. 2871–2875.PubMedGoogle Scholar
  29. 29.
    Liuni, S., Prunella, N., Pesole, G., et al., Comput. Appl. Biosci., 1993, vol. 9, pp. 701–707.PubMedGoogle Scholar
  30. 30.
    Hertz, G.Z. and Stormo, G.D., Bioinformatics, 1999, vol. 15, pp. 563–577.PubMedGoogle Scholar
  31. 31.
    Pevzner, P.A. and Sze, S.-H., '2000, 2000, pp. 269–278.Google Scholar
  32. 32.
    Jonassen, I., Comput. Appl. Biosci., 1997, vol. 13, pp. 509–522.PubMedGoogle Scholar
  33. 33.
    Brazma, A., Jonassen, I., Vilo, J., and Ukkonen, E., Genome Res., 1998, vol. 8, pp. 1202–1215.PubMedGoogle Scholar
  34. 34.
    Marsan, L. and Sagot, M.-F., '2000, 2000, pp. 210–219.Google Scholar
  35. 35.
    Ulyanov, A.V. and Stormo, G.D., Nucleic Acids Res., 1995, vol. 23, pp. 1434–1440.PubMedGoogle Scholar
  36. 36.
    Fraenkel, Y.M., Mandel, Y., Friedberg, D., and Margalit, H., Comput. Appl. Biosci., 1995, vol. 11, pp. 379–387.PubMedGoogle Scholar
  37. 37.
    Rocke, E. and Tompa, M., Proc. 2nd Annu. Int. Conf. on Computational Molecular Biology RECOMB'98, 1998, pp. 228–233.Google Scholar
  38. 38.
    Tompa, M., Proc. 7th Int. Conf. on Intelligent Systems for Molecular Biology ISMB'1999, 1999, pp. 262–271.Google Scholar
  39. 39.
    Rigoutsos, I. and Floratos, A., Bioinformatics, 1998, vol. 14, pp. 55–67.CrossRefPubMedGoogle Scholar
  40. 40.
    van Helden, J., Andre, B., and Collado-Vides, J., J. Mol. Biol., 1998, vol. 281, pp. 827–842.PubMedGoogle Scholar
  41. 41.
    Jensen, L.J., Knudsen, S., Bioinformatics, 2000, vol. 16, pp. 326–333.CrossRefPubMedGoogle Scholar
  42. 42.
    Cho, R.J., Campbell, M.J., Winzeler, E.A., et al., Molecular Cell, 1998, vol. 2, pp. 65–73.CrossRefPubMedGoogle Scholar
  43. 43.
    Wolfsberg, T.G., Gabrielian, A.E., Campbell, M.J., et al., Genome Res., 1999, vol. 9, pp. 775–792.PubMedGoogle Scholar
  44. 44.
    V'yugin, V.V., Gorbunov, K.Yu., and Lyubetskii, V.A., Trudy konferentsii “Problemy upravleniya i modelirovaniya v slozhnykh sistemakh” (Proc. Conf. “Controlling and Simulation Problems in Complex Systems”), Myasnikov, V.P., Ed., Moscow: Ross. Akad. Nauk, 2000, pp. 130–137.Google Scholar
  45. 45.
    Robison, K., McGuire, A.M., and Church, G.M., J. Mol. Biol., 1998, vol. 284, pp. 241–254.PubMedGoogle Scholar
  46. 46.
    Mironov, A.A., Vinokurova, N.P., and Gel'fand, M.S., Mol. Biol., 2000, vol. 34, pp. 253–264.Google Scholar
  47. 47.
    Maas, W.K., Microbiol. Rev., 1994, vol. 58, pp. 631–640.PubMedGoogle Scholar
  48. 48.
    Busby, S. and Kolb, A., Regulation of Gene Expression in Escherichia coli, Lin, E.C.C. and Lynch, A.S., Eds., E.G. Landes, 1995, ch. 12, pp. 255–279.Google Scholar

Copyright information

© MAIK “Nauka/Interperiodica” 2001

Authors and Affiliations

  • L. V. Danilova
    • 1
  • K. Yu. Gorbunov
    • 1
  • M. S. Gelfand
    • 2
  • V. A. Lyubetskii
    • 1
  1. 1.Institute of Problems of Data Transmission, Russian Academy of SciencesMoscowRussia
  2. 2.State Research Center of GeneticsMoscowRussia

Personalised recommendations