Latent sequence periodicity of some oncogenes and dna-binding protein genes

Bioinformatics

Volumn 13, Issue 1, 1997, Pages 37-44

  Korotkov, E V ^a,b   Tuiko, J S ^a,b  

^a RUSSIAN ACADEMY OF SCIENCES   (Russian Federation)

^b NATIONAL RESEARCH NUCLEAR UNIVERSITY MEPHI   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; MESSENGER RNA;

ARTICLE; GENE SEQUENCE; ONCOGENE; PERIODICITY; PRIORITY JOURNAL; RNA SEQUENCE; TUMOR SUPPRESSOR GENE;

ANIMALS; BASE SEQUENCE; COMPUTERS; DATABASES, FACTUAL; DNA; DNA-BINDING PROTEINS; HUMANS; MATHEMATICS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; ONCOGENES; REPETITIVE SEQUENCES, NUCLEIC ACID; RNA, MESSENGER;

EID: 0030963554     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/13.1.37     Document Type: Article

References (36)

1. Acampora, D., D'Esposito, M., Faiella, A., Pannese, M., Migliaccio, E., Mor-elli, F., Stornaiuolo, A., Nigro, V., Simeone, A. and Boncinelli, E. (1989) The human hox gene family. Nucleic Acids Res., 17, 10385-10409.
2. BeckJ.W., Huleihel, M., BonnerJ.I. and Rapp.U.R. (1987) The complete coding sequence of the human A-RAF-1 oncogene and transforming activity of a human A-RAF carrying retrovirus. Nucleic Acids Res., 15, 595-609.
3. Bina.M. (1994) Periodicity of dinucleotides in nucleosomes derived from Simian virus 40 chromatin. J. Mol. Biol, 235, 198-208.
4. Bliskovsky, V.V. (1991) Tandem DNA repeats in vertebrate genomes: structure, possible mechanisms of creation and evolution. Mol. Biol. (Russian), 25, 965-982.
5. Borstnik, B., Pampernik, D., Lukman.D., Ugarkovic.D. and Plohl, M. (1994) Tandemly repeated pentanucleotides in DNA sequences of eukaryotes. Nucleic Acids Res., 22, 3412-3417.
6. Carrera, P. and Azorin.F. (1994) Structural characterization of intrinsically curved AT-rich DNA sequences. Nucleic Acids Res., 22, 3671—3680.
7. Chechetkin.V.R., Knizhnikova, L.A. and Turygin.A.Yu. (1994) Three-quasiperiodicity, mutual correlations, ordering and long modulations in genomic nucleotide sequences of viruses. J. Biomol. Struct. Dynam., 12, 271-299.
8. Cheever.E.A., Overton, G.C. and Searls, B.B. (1991) Fast fourier transform-based correlations of DNA sequences using complex plane encoding. Comput. Applic. Biosci., 7, 143—154.
9. Coussens.L., Van Beveren.C, Smith.D., Chen.E., Mitchell, R.L., Isack-e, C.M., Verma, I.M,. and Ullrich, A. (1986) Structural alternation of viral homologue of receptor proto-oncogene FMS at carboxyl terminus. Nature, 320, 277-280.
10. Fainstein, E., Einat, M., Gokkel, E., Marcelle, C, Croce, C.M, Gale.R.P and Canaani.E. (1989) Nucleotide sequence analysis of human ABL and BCR-ABL cDNA's. Oncogene, 4, 1477-1481.
11. Gehring, W.J., Qian, Y.Q., Billeter.M., Furucubo-Tokunaga.K., Schier, A.F., Resendez-Perez.D., Affolter.M., Otting.G. and Wuthrich.K. (1994) Home-odomain-DNA recognition. Cell, 78, 211-223.
12. Goodsell, D.S. and Dickerson, R.E. (1994) Bending and curvature calculations in B+DNA. Nucleic Acids Res., 22, 5497-5503.
13. andboot o/App/i'caWeA/af/iemarici (1984) Wiley-Interscience, John Wiley & Sons, New York, Vol. IV.
14. Heame.C.M., Ghosh.S. and Todd, J.A. (1992) Microsatellites for linkage analysis of genetic traits. Trends Genet., 8, 288—294.
15. Kadonaga, J.T., Carner, K.R., Masiarz.F.R. and Tjian.R. (1987) Isolation of cDNA encoding transcription factor SP1 and functional analysis of the DNA binding domain. Cell, 51, 1079-1090.
16. Kinzler, K.W., Ruppert.J.M., Bigner, S.H. and Vogelstein.B. (1988) The GL1 gene is a member of the kruppel family of zinc finger proteins. Nature, 332, 371-374.
17. Korotkov, E.V. (1994) Fast method of homology and purine-pyrimidine mutual relations between DNA sequences search. DNA Sequence, 4, 413-415.
18. Korotkov, E.V. and Korotkova, M.A. (1993) Enlarged similarity of nucleic acids sequences. Preprint of Moscow Physical Engineering Institute, N.012-93, Moscow.
19. Korotkov.E.V. and Korotkova, M.A. (1995) Latent periodicity of DNA sequences of some human genes. DM4 Sequence, 5, 353—358.
20. Kullback, S. (1959) Information Theory and Statistics. John Wiley & Sons, New York.
21. Lee.W.H., Shew, J.Y., Hong, F.D., Sery.T.W., Donoso, L.A., Young, L.J., Bookstein, R. and Lee, E.Y.H.P. (1987) The retinoblastoma susceptibility gene encodes a nuclear phosphoprotein associated with DNA binding activity. Nature, 329, 642-645.
22. Makeev, V.Ju. and Tumanyan, V.G. (1994) On a link between the distance and correlation analysis of various types and Fourier transformation used for the search of the periodical patterns in the primary structures of the biopolymers. Biophysics (Russian), 39, 294-297.
23. McLachlan, A.D. (1977a) Repeated helical pattern in apolipoprotein A-l. Nature, 267, 465-466.
24. McLachlan.AD. (1977b) Analysis of periodic patterns in amino acid sequences: collagen. Biopolymers, 16, 1271-1297.
25. McLachlan.A.D. (1993) Multichannel Fourier analysis of patterns in protein sequences. J. Phys. Chem., 97, 3000-3006.
26. McLachlan, AD and Stewart.M. (1994) Analysis of repeated motif in the talin rod. J. Mol. Bio!., 235, 1278-1290.
27. McNamara, P.T., Bolshoy, A, Trifonov, E.N. and Harrington, R.E. (1990) Sequence-dependent kinks in curved DNA. J. Biomol. Struct. Dynam., 3, 529-538.
28. Merlino, G.T., Ishii, S., Whang-Peng, J., Knutsen, T., Xu, Y.H., Clark, A.J.L., Stratton, R.H., Wilson, R.K., Ma, D.P., Roe, B.A., Hunts, J.H., Shimizu, N. and Pastan, I. (1985) Structure and localization of genes encoding aberrant and normal epidermal growth factor receptor RNAs from A431 human carcinoma cells. Mol. Cell. Biol., 5, 1722-1734.
29. Pizzi.E., Linni.S. and Frontali.C. (1990) Detection of latent sequence periodicities. Nucleic Acids Res., 18, 3745-3752.
30. Silverman.B.D. and Linsker.R. (1986) A measure of DNA periodicity. J. Theor. Biol., 118, 295-300.
31. Simeone A, Mavilio, F., Acampora, D., Giampaolo A, Faiella A, Zappavigna, V., D'Esposito, M., Pannese, M., Russo, G., Boncinelli.E. and Peschle.C. (1987) Two human homeobox genes, Cl and C8: structure analysis and expression in embryonic development. Proc. NatlAcad. Set USA, 84, 4914-4918.
32. Stewart.M. and McLachlan, A.D.(1975) Fourteen actin-binding sites on tropomyosin? Nature, 257, 331-333.
33. ToddJ.A. (1992) La carte des microsatellites est arrivee. Hum. Mol. Genet., I, 663-666.
34. von Heijne.G. (1987) Sequence Analysis in Molecular Biology. Academic Press, San Diego, CA.
35. Voss.R.F. (1992) Evolution of long-range fractal correlations and 1/f noise in DNA base sequences. Phys. Rev. Lett., 68, 3805-3808.
36. Yaglom, A.M. and Yaglom, I.M. (1960) Probability and Information. Nauka Press, Moscow.