The informational concept of searching for periodicity in symbol sequences

Molekulyarnaya Biologiya

Volumn 37, Issue 3, 2003, Pages 436-451

  Korotkov, E V ^a   Korotkova, M A ^b   Frenkel, F E ^a   Kudryashov, N A ^b  

^a INSTITUTE OF BIOENGINEERING   (Russian Federation)

^b NATIONAL RESEARCH NUCLEAR UNIVERSITY MEPHI   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; GENE FUNCTION; GENE STRUCTURE; GENETIC VARIABILITY; NUCLEOTIDE SEQUENCE; PERIODICITY; PROTEIN FUNCTION; ALGORITHM; INFORMATION SCIENCE; LITERATURE; MATHEMATICAL COMPUTING; METHODOLOGY;

ALGORITHMS; AMINO ACID SEQUENCE; BASE SEQUENCE; INFORMATION SCIENCE; MATHEMATICAL COMPUTING; PERIODICITY; POETRY;

EID: 0141722809     PISSN: 00268984     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (70)

1. Pennisi E. 2001. The Human Genome. Science. 291, 1177-1180.
2. Benson D.A., Karsch-Mizrachi I., Lipman D.J. et al. 2000. GenBank. Nucleic Acids Res. 28, 15-18.
3. Stoesser G., Baker W., van den Broek A. et al. 2001. The EMBL nucleotide sequence database. Nucleic Acids Res. 29, 17-21.
4. Junker V., Contrino S., Fleischmann W. et al. 2000. The role SWISS-PROT and TrEMBL play in the genome research environment. J. Biotechnol. 78, 221-234.
5. Adams M.D., Celniker S.E., Holt R.A. et al. 2000. The Genome sequence of Drosophila melanogaster. Science. 287, 2185-2195.
6. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature. 409, 860-921.
7. Venter J.C., Adams M.D., Myers E.W. et al. 2001. The sequence of the human genome. Science. 291, 1304-1351.
8. Marple S.L. 1987. Digital spectral analysis with applications. Englewood Cliffs, New-Jersey:Prentice-Hall, Inc.
9. Dodin G., Vandergheynst P., Levoir P. et al. 2000. Fourier and wavelet transform analysis, a tool for visualizing regular patterns in DNA sequences. J. Theor. Biol. 206, 323-326.
10. Jackson J.H., George R., Herring P.A. 2000. Vectors of Shannon information from Fourier signals characterizing base periodicity in genes and genomes. Biochem. Biophys. Res. Commun. 268, 289-292.
11. Rackovsky S. 1998. Hidden' sequence periodicities and protein architecture. Proc. Natl. Acad. Sci. USA. 95, 8580-8584.
12. Chechetkin V.R., Lobzin V.V. 1998. Nucleosome units and hidden periodicities in DNA sequences. J. Biomol. Struct. Dyn. 15, 937-947.
13. Coward E., Drablos F. 1998. Detecting periodic patterns in biological sequences. Bioinformatics. 14, 498-507.
14. Voss R.F. 1992. Evolution of long range fractal correlations and 1/f noise in DNA base sequences. Phys. Rev. Lett. 25, 3805-3808.
15. Silverman B.D., Linsker R. 1996. A measure of DNA periodicity. J. Theor. Biol. 118, 295-300.
16. McLachlan A.D. 1993. Multichannel Fourier analysis of patterns in protein sequences. J. Phys. Chem. 97, 3000-3006.
17. Makeev V.Ju., Tumanyan V.G. 1994. On 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. 39, 294-297.
18. Makeev V.Ju., Tumanyan V.G. 1996. Search of periodicities in primary structure of biopolymers: a general Fourier approach. Comput. Appl. Biosci. 12, 49-54.
19. Korotkov E.V., Korotkova M.A. 1995. DNA regions with latent periodicity in some human clones. DNA Sequence. 5, 353-358.
20. Korotkov E.V., Korotkova M.A., Tulko J.S. 1997. Latent sequence periodicity of some oncogenes and DNA-binding protein genes. CABIOS. 13, 37-44.
21. Chaley M.B., Korotkov E.V., Skryabin K.G. 1999. Method reavealing latent periodicity of the nucleotide sequences modified for a case of small samples. DNA Research. 6, 153-163.
22. Korotkova M.A., Korotkov E.V., Rudenko V.M. 1999. Latent periodicity of protein sequences. J. Mol. Modelling. 5, 103-115.
23. Kullback S. 1959. Information theory and Statistics. N.-Y., London: John Wiley & Sons, Inc.
24. Handbook of Applicable Mathematics. Part A. 1984. Ed. Lloyd E. New-York-Brisbane-Toronto-Singapore: A Wiley Intersci. Publ., John Wiley & Sons.
25. Hertz G.Z., Stormo G.D. 1999. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformafics. 15, 563-577.
26. Tiwari S., Ramachandran S., Bhattacharya A. et al. 1997. Prediction of probable genes by Fourier analysis of genomic sequences. CABIOS. 13, 263-270.
27. Ramakrishna R., Srinivasan R. 1999. Gene identification in bacterial and organellar genomes using GeneScan. Computers and Chemistry. 23, 165-174.
28. Benson G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573-580.
29. Grosse I., Herzel H., Buldyrev S.V., Stanley H.E. 2000. Species independence of mutual information in coding and noncoding DNA. Phys. Rev. E. 61, 5624-5629.
30. Herzel H., Grosse I. 1995. Measuring correlations in symbolic sequences. Physica A. 216, 518-542.
31. Almirantis Y., Provata A. 1999. Long- and short-range correlations in genome organization. J. Stat. Phys. 97, 233-262.
32. Tettelin H., Saunders N.J., Heidelberg J. et al. 2000. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science. 287, 1809-1815.
33. Redenbach M., Kieser H.M., Denapaite D. et al. A set of ordered cosmids and a detailed genetic and physical map for the 8 Mb Streptomyces coelicolor A3 (2) chromosome. Mol. Microbiol. 21, 77-96.
34. Herzel H., Trifonov E.N., Weiss O., Große I. 1998. Interpreting correlations in biosequences. Physica A. 249, 449-459.
35. Heringa J. 1998. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Current Opin. Struct. Biol. 8, 338-345.
36. Trifonov E.N. 1998. 3-, 10.5-, 200- and 400-base periodicities in genome sequences. Physica A. 249, 511-516.
37. Weiss O., Herzel H. 1998. Correlations in protein sequences and property codes. J. Theor. Biol. 190, 341-353.
38. Trifonov E.N. 1989. The multiple codes of nucleotide sequences. Bull. Math. Biol. 51, 417-432.
39. Li W., Kaneko K. 1992. Long-range correlation and partial 1/f spectrum in a noncoding DNA sequence. Europhys. Lett. 17, 655-660.
40. Peng C.K., Buldyrev S., Goldberger A.L. et al. 1992. Long-range correlations in nucleotide sequences. Nature. 356, 168-170.
41. Chatzidimitriou-Dreismann C.A., Larhammar D. 1993. Long-range correlations in DNA. Nature. 361, 212-213.
42. Prabhu V.V., Claverie J.M. 1992. Correlations in intron-less DNA. Nature. 359, 782-786.
43. Karlin S., Brendel V. 1993. Patchiness and correlations in DNA sequences. Science. 259, 677-680
44. Luo L., Lee W., Jia L. et al. 1998. Statistical correlation of nucleotides in a DNA sequence. Phys. Rev. E. 58 861-871.
45. Yu Z.-G., Chen G.-Y. 2000. Rescaled range and transition matrix analysis of DNA sequences. Commun. Theor. Phys. 33, 673-678.
46. Voss R. 1994. Long-range fractal correlations in DNA introns and exons. Fractals. 2, 1-6.
47. Stanley H.E., Buldyrev S.V., Goldberg A.L. et al. 1994. Statistical mechanics in biology: how ubiquitous are long-range correlations? Physica A. 205, 214-253.
48. Herzel H., Ebeling W., Sehmitt A.O. 1994. Entropies of biosequences - the role of repeats. Phys. Rev. E. 50, 5061-5071.
49. Allegrini P., Barbi M., Grigolini P., West B-J. 1995. A dynamical model for DNA sequences. Phys. Rev. E. 52, 5281-5293.
50. Buldyrev S.V., Goldberger A.L., Havlin S. et al. 1995. Long-range correlation properties of coding and noncoding DNA sequences: GenBank analysis. Phys. Rev. E. 51, 5084-5091.
51. Arneodo A., Bacry E., Graves P.V., Muzy J.F. 1995. Characterizing long-range correlations in DNA sequences from wavelet analysis. Phys. Rev. Lett. 74, 3293-3296.
52. Mohanty A.K., Narayana Rao S.S. 2000. Factorial moments analyses show a characteristic length scale in DNA sequences. Phys. Rev. Lett. 84, 1832-1835.
53. Conway J.F., Parry D.A. 1990. Structural features in the heptad substructure and longer range repeats of two-stranded α-fibrous proteins. Int. J. Biol. Macromol. 12, 328-334.
54. Presta L.G., Rose G.D. 1988. Helix signals in proteins. Science. 240, 1632-1641.
55. Audit B., Thermes C., Vaillant C. et al. 2001. Long-range correlations in genomic DNA: a signature of the nucleosomal structure. Phys. Rev. Lett. 86, 2471-2474.
56. Matsumoto T., Funk C.D., Radmark O. et al. 1988. Molecular cloning and amino acid sequence of human 5-lipoxygenase. Proc. Natl. Acad. Sci. USA. 85, 26-30.
57. Ochiai H., Inoue Y., Hasebe A., Kaku H. 2001. Construction and characterization of a Xanthomonas oryzae pv. oryzae bacterial artificial chromosome library. FEMS Microbiol. Lett. 200, 59-65.
58. Parkhill J., Achtman M., James K.D. et al. 2000. Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491. Nature. 404, 502-506.
59. Iannelli F., Oggioni M.R., Pozzi G. 2002. Allelic variation in the highly polymorphic locus pspC of Streptococcus pneumoniae. Gene. 284, 63-71.
60. Smith D.R., Doucette-Stamm L.A., Deloughery C. et al. 1997. Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics. J. Bacteriol. 179, 7135-7155.
61. Cachon-González M.B., Fenner S., Coffin J.M. et al. 1994. Structure and expression of the hairless gene of mice. Proc. Natl. Acad. Sci. USA. 91, 7717-7721.
62. Hauser L.J., Treat M.L., Olins D.E. 1993. Cloning and analysis of the macronuclear gene for histone H1 from Euplotes eurystomus. Nucleic Acids Res. 21, 3586-3594.
63. Abo H., Matsumura T., Kodama T. et al. 1991. Peptide sequences for sucrose splitting and glucan binding within Streptococcus sobrinus glucosyltransferase (water-insoluble glucan synthetase). J. Bacteriol. 173, 989-996.
64. Bhandari V., Palfree R.G., Bateman A. 1992. Isolation and sequence of the granulin precursor cDNA from human bone marrow reveals tandem cysteine-rich granulin domains. Proc. Natl. Acad. Sci. USA. 89, 1715-1719.
65. Yamazaki N., Shinohara Y., Shima A., Terada H. 1995. High expression of a novel carnitine palmitoyltransferase I like protein in rat brown adipose tissue and heart: isolation and characterization of its cDNA clone. FEBS Lett. 363, 41-45.