Repeats and correlations in human DNA sequences

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 67, Issue 6 1, 2003, Pages

  Holste, Dirk ^a   Grosse, Ivo ^b   Beirer, Stephan ^c   Schieg, Patrick ^c   Herzel, Hanspeter ^c  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^c HUMBOLDT UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

APPROXIMATION THEORY; CHROMOSOMES; DNA SEQUENCES; MATHEMATICAL MODELS; MOLECULAR STRUCTURE; RANDOM PROCESSES; STATISTICAL METHODS;

HUMAN GENOME; NUCLEOTIDE-NUCLEOTIDE MUTUAL INFORMATION FUNCTION; PROTEIN CODING SEQUENCE;

MOLECULAR BIOLOGY;

DNA;

ALU SEQUENCE; BIOPHYSICS; CHEMISTRY; CHROMOSOME; COMPUTER SIMULATION; CONFORMATION; HEAT; HUMAN; NUCLEOTIDE REPEAT; PRESSURE; PROCEDURES; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; STATISTICAL MODEL; TEMPERATURE; THERMODYNAMICS; TIME; ULTRASTRUCTURE;

ALU ELEMENTS; BIOPHYSICS; CHROMOSOMES; COMPUTER SIMULATION; DNA; HOT TEMPERATURE; HUMANS; MODELS, STATISTICAL; NUCLEIC ACID CONFORMATION; PRESSURE; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; REPETITIVE SEQUENCES, NUCLEIC ACID; TEMPERATURE; THERMODYNAMICS; TIME FACTORS;

EID: 42749101835     PISSN: 1063651X     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (73)

1. W.-H. Li, Molecular Evolution (Sinauer Associates, Sunderland, MA, 1997).
2. Computational Models in Molecular Biology, edited by S.L. Salzberg, D.B. Searls, and S. Kasif (Elsevier, Amsterdam, 1998).
3. J.K. Percus, Mathematics of Genome Analysis (Columbia University Press, Cambridge, 2002).
4. D.E. Reich et al., Nat. Genet. 32, 135 (2002).
5. R. Staden and A.D. McLachlan, Nucleic Acids Res. 10, 141 (1982)
6. J.W. Fickett, ibid. 10, 5303 (1982)
7. J.W. Fickett and C.-S. Tung, ibid. 20, 6441 (1992)
8. M.S. Gelfand, J. Comput. Biol. 2, 87 (1995)
9. I. Groose et al., Phys. Rev. E 61, 5624 (2000)
10. D. Holste et al., J. Theor. Biol. 206, 525 (2000).
11. E.N. Trifonov and J.L. Sussman, Proc. Natl. Acad. Sci. U.S.A. 77, 3813 (1980).
12. H. Herzel, O. Weiss, and E.N. Trifonov, Bioinformatics 15, 187 (1999).
13. V.B. Zhurkin, J. Biomol. Struct. Dyn. 4, 785 (1981).
14. O. Weiss and H. Herzel, J. Theor. Biol. 190, 341 (1998).
15. S.V. Buldyrev et al., Biophys. J. 65, 2673 (1993).
16. B. Audit et al., Phys. Rev. Lett. 86, 2471 (2001)
17. B. Audit et al., J. Mol. Biol. 316, 903 (2002).
18. W. Li, Gene 300, 129 (2002).
19. J. Filipski, J.P. Thiery, and G. Bernardi, J. Mol. Biol. 80, 177 (1973).
20. G. Bernardi et al., Science 288, 953 (1985)
21. G. Bernardi, Gene 241, 3 (2000).
22. W. Li and K. Kaneko, Europhys. Lett. 17, 655 (1992)
23. C.-K. Peng et al., Nature (London) 356, 168 (1992)
24. R.F. Voss, Phys. Rev. Lett. 68, 3805 (1992)
25. S.V. Buldyrev et al. Phys. Rev. E 51, 5084 (1995).
26. W. Li, T.G. Marr, and K. Kaneko, Physica D 75, 395 (1994)
27. W. Li, Comput. Chem. (Oxford) 21, 257 (1997).
28. D. Holste, I. Grosse, and H. Herzel, Phys. Rev. E 64, 041917 (2001).
29. E. Lander et al., Nature (London) 409, 860 (2001).
30. J.C. Venter et al., Science 291, 1904 (2001).
31. G.K.-S. Wong et al., Genome Res. 10, 1672 (2000)
32. M. Das et al., Genomics 77, 71 (2001)
33. N. Katsanis, K.C. Worley, and J.R. Lupski, Nat. Genet. 29, 88 (2001).
34. We downloaded the DNA sequences of human chromosomes 20 21, and 22 from ftp://ftp.ensembl.org/pub/, which have been assembled in version v3.26.1. Human chromosomes 20 21, and 22 are almost complete and updated versions of these three chromosomes undergo only minor modifications. We excluded all presently unknown nucleotides due to gaps in the sequences.
35. C.E. Shannon, Bell Syst. Tech. J. 27, 379 (1948).
36. W. Ebeling, R. Feistel, and H. Herzel, Phys. Ser. 35, 761 (1987).
37. H. Herzel and I. Grosse, Phys. Rev. E 55, 800 (1997).
38. G.A. Miller, Information Theory in Psychology, edited by H. Quaster (Free Press, Glencoe, 1955)
39. G.P. Basharin, Theor. Probab. Appl. 4, 333 (1959)
40. M.S. Roulston, Physica D 125, 285 (1999).
41. I. Dunham et al., Nature (London) 402, 489 (1999)
42. M. Hattori et al., ibid. 405, 311 (2000)
43. P. Deloukas et al., ibid. 414, 865 (2001)
44. J.E. Collins et al., Genome Res. 13, 27 (2003).
45. A. Nekrutenko and W.-H. Li, Genome Res. 10, 1986 (2000).
46. D. Häring and J. Kypr, Biochem. Biophys. Res. Commun. 280, 567 (2001).
47. O. Clay et al., Gene 276, 15 (2001).
48. 2
49. A.F.A. Smith, Curr. Opin. Genet. Dev. 6, 743 (1996)
50. A.F.A. Smit, ibid. 9, 657 (1999).
51. P. Sudbery, Human Molecular Genetics (Addison Wesley Longman, Singapore, 1998).
52. M.A. Batzer and P.L. Deininger, Nat. Rev. Genet. 3, 370 (2002).
53. We use repeatmasker version v07072001. A.F.A. Smit and P. Green. Accessible at World-wide web http://repeatmasker.genome.washington.edu/
54. J.E. Stenger et al., Genome Res. 11, 12, (2001).
55. A. Nekrutenko and W.-H. Li, Trends Genet. 17, 619 (2001)
56. R. Sorek et al., Genome Res. 12, 1060 (2002).
57. J.R. Korenberg and M.C. Rykowski, Cell 53, 391 (1988).
58. P. Medstrand et al., Genome Res. 12, 1483 (2002).
59. W.M. Chu et al., Mol. Cell. Biol. 18, 58 (1998).
60. M.-A. Hakimi et al., Nature (London) 418, 994 (2002).
61. F. Jeanmougin et al., Trends Biochem. Sci. 23, 403 (1998) Accessible at ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/
62. C.R. Calladine and H.R. Drew, Understanding DNA (Academic Press, London, 1992).
63. A. Bolshoy et al., Proc. Natl. Acad. Sci. U.S.A. 88, 2312 (1991).
64. jε W, 0 else) defines the WW-WW autocorrelation function.
65. -1 = 10-11 bp.
66. K.E. van Holde, Chromatin (Springer-Verlag, New York, 1988).
67. R.L.P. Adams et al., Eur. J. Biochem. 165, 105 (1987).
68. D. Takai and P.A. Jones, Proc. Natl. Acad. Sci. U.S.A. 99, 3740 (2002).
69. K. Jabbari and G. Bernardi, Gene 224, 123 (1998).
70. P. Green, Genome Res. 7, 410 (1997).
71. A. Eyre-Walker and L.D. Hurst, Nat. Rev. Genet. 2, 549 (2001).
72. K.J. Fryxell and E. Zuckerkandl, Mol. Biol. Evol. 17, 1371 (2000).
73. I. Grosse, M. Zhang, and H. Herzel (unpublished)