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.
Similar content being viewed by others
References
Spellman, P.T. et al., Mol. Biol. Cell, 1998, vol. 9, pp. 3273–3297.
Roth, F.R. et al., Nature Biotechnol., 1998, vol. 16, pp. 939–945.
Bassett, D.E. Jr. et al., Nature Genet., 1999, vol. 21, pp. 51–55.
Bucher, P., Curr. Opin. Struct. Biol., 1999, vol. 9, pp. 400–407.
Gelfand, M.S., Koonin, E.V., and Mironov, A.A., Nucleic Acids Res., 2000, vol. 28, pp. 695–705.
McGuire, A.M., Hughes, J.D., and Church, G.M., Genome Res., 2000, vol. 10, pp. 744–757.
Gelfand, M.S., Res. Microbiol., 1999, vol. 150, pp. 755–771.
Gelfand, M.S., J. Comput. Biol., 1995, vol. 2, pp. 87–115.
Frech, K., Quandt, K., and Werner, T., Comput. Appl. Biosci., 1997, vol. 13, pp. 89–97.
Duret, L. and Bucher, P., Curr. Opin. Struct. Biol., 1997, vol. 7, pp. 399–406.
Fickett, J.W. and Wasserman, W.W., Curr. Opin. Biotechnol., 2000, vol. 11, pp. 19–24.
Stormo, G.D. and Hartzell, G.W. III., Proc. Natl. Acad. Sci. USA, 1989, vol. 86, pp. 1183–1187.
Hertz, G.Z., Hartzell, G.W. III, and Stormo, G.D., Comput. Appl. Biosci., 1990, vol. 6, pp. 81–92.
Lawrence, C.E. and Reilly, A.A., PROTEINS: Structure, Function, Genetics, 1990, vol. 7, pp. 41–51.
Cardon, L.R. and Stormo, G.D., J. Mol. Biol., 1992, vol. 223, pp. 159–170.
Frishman, D., Mironov, A., Gelfand, M., Gene, 1999, vol. 234, pp. 257–265.
Gelfand, M.S., Koonin, E.V., and Mironov, A.A., Nucleic Acids Res., 2000, vol. 28, pp. 695–705.
Hu, Y.-J., Sandmeyer, S., McLaughlin, C., and Kibler, D., Bioinformatics, 2000, vol. 16, pp. 222–232.
Bailey, T.L. and Elkan, C.P., Proc. 2nd Int. Conf. on Intelligent Systems for Molecular Biology ISMB'1994, 1994, pp. 28–36.
Bailey, T.L. and Elkan, C.P., Proc. 3rd Int. Conf. on Intelligent Sysems for Molecular Biology ISMB'1995, 1995, pp. 21–29.
Grundy, W.N., Bailey, T.L., and Elkan, C.P., Comput. Appl. Biosci., 1996, vol. 12, pp. 303–310.
Lukashin, A.V., Engelbrecht, J., and Brunak, S., Nucleic Acids Res., 1992, vol. 20, pp. 2511–2516.
Lawrence, C.E., Altschul, S.F., Boguski, M.S., et al., Science, 1993, vol. 262, pp. 208–214.
Roth, F.P., Hughes, D., Estep, P.W., and Church, G.M., Nature Biotech., 1998, vol. 16, pp. 939–945.
Frech, K., Herrmann, G., and Werner, T., Nuceic. Acids Res., 1993, vol. 21, pp. 1655–1664.
Quandt, K., Frech, K., Karas, H., et al., Nucleic Acids Res., 1995, vol. 23, pp. 4878–4884.
Kielbasa, Sz.M., Korbel, J.O., Beule D., et al., '2000, 2000, pp. 55–62.
Pesole, G., Prunella, N., Liuni S., et al., Nucleic Acids Res., 1992, vol. 20, pp. 2871–2875.
Liuni, S., Prunella, N., Pesole, G., et al., Comput. Appl. Biosci., 1993, vol. 9, pp. 701–707.
Hertz, G.Z. and Stormo, G.D., Bioinformatics, 1999, vol. 15, pp. 563–577.
Pevzner, P.A. and Sze, S.-H., '2000, 2000, pp. 269–278.
Jonassen, I., Comput. Appl. Biosci., 1997, vol. 13, pp. 509–522.
Brazma, A., Jonassen, I., Vilo, J., and Ukkonen, E., Genome Res., 1998, vol. 8, pp. 1202–1215.
Marsan, L. and Sagot, M.-F., '2000, 2000, pp. 210–219.
Ulyanov, A.V. and Stormo, G.D., Nucleic Acids Res., 1995, vol. 23, pp. 1434–1440.
Fraenkel, Y.M., Mandel, Y., Friedberg, D., and Margalit, H., Comput. Appl. Biosci., 1995, vol. 11, pp. 379–387.
Rocke, E. and Tompa, M., Proc. 2nd Annu. Int. Conf. on Computational Molecular Biology RECOMB'98, 1998, pp. 228–233.
Tompa, M., Proc. 7th Int. Conf. on Intelligent Systems for Molecular Biology ISMB'1999, 1999, pp. 262–271.
Rigoutsos, I. and Floratos, A., Bioinformatics, 1998, vol. 14, pp. 55–67.
van Helden, J., Andre, B., and Collado-Vides, J., J. Mol. Biol., 1998, vol. 281, pp. 827–842.
Jensen, L.J., Knudsen, S., Bioinformatics, 2000, vol. 16, pp. 326–333.
Cho, R.J., Campbell, M.J., Winzeler, E.A., et al., Molecular Cell, 1998, vol. 2, pp. 65–73.
Wolfsberg, T.G., Gabrielian, A.E., Campbell, M.J., et al., Genome Res., 1999, vol. 9, pp. 775–792.
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.
Robison, K., McGuire, A.M., and Church, G.M., J. Mol. Biol., 1998, vol. 284, pp. 241–254.
Mironov, A.A., Vinokurova, N.P., and Gel'fand, M.S., Mol. Biol., 2000, vol. 34, pp. 253–264.
Maas, W.K., Microbiol. Rev., 1994, vol. 58, pp. 631–640.
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.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Danilova, L.V., Gorbunov, K.Y., Gelfand, M.S. et al. Algorithm of Regulatory Signal Recognition in DNA Sequences. Molecular Biology 35, 841–848 (2001). https://doi.org/10.1023/A:1013282101105
Issue Date:
DOI: https://doi.org/10.1023/A:1013282101105