A study of the middle-scale nucleotide clustering in DNA sequences of various origin and functionality, by means of a method based on a modified standard deviation

Journal of Theoretical Biology

Volumn 217, Issue 4, 2002, Pages 479-492

  Nikolaou, Christoforos ^a   Almirantis, Yannis ^a  

^a Natl Res Ctr for Phys Sci D   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NUCLEOTIDE; PROTEIN; RIBOSOME RNA; SPACER DNA;

DNA;

ARTICLE; CODING; DNA SEQUENCE; EUKARYOTE; EVOLUTION; GENE CLUSTER; GENE FREQUENCY; GENE FUNCTION; GENETIC CODE; GENOME; INTRON; METHODOLOGY; NOMENCLATURE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PARAMETER; PRIORITY JOURNAL; PROKARYOTE; PROMOTER REGION; SACCHAROMYCES CEREVISIAE; STATISTICAL ANALYSIS;

EUKARYOTA; PROKARYOTA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0036401272     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1006/jtbi.2002.3045     Document Type: Article

References (49)

1. Almirantis, Y. (1999). A standard deviation based quantification differentiates coding from non-coding DNA sequences and gives insight to their evolutionary history. J. theor. Biol. 196, 297-308.
2. Almirantis, Y. & Provata, A. (1999). Long- and short-range correlations in genome organisation. J. Stat. Phys. 97, 233-262.
3. Almirantis, Y. & Provata, A. (2001). An evolutionary model for the origin of non-randomness, long-range order and fractality in the genome. BioEssays 23, 647-656.
4. Audit, B., Thermes, C., Vaillant, C., D'Aubenton-Carafa, Y., Muzy J. F. & Arneodo, A. (2001). Long-range correlations in genomic DNA: a signature of the nucleosomal structure. Phys. Rev. Lett. 86, 2471-2474.
5. Berg, A. G. (1995). Kinetics of synonymous codon change for an aminoacid of arbitrary degeneracy. J. Mol. Evol. 41, 345-352.
6. Bernardi, G. (1993). Genome organization and species formation in vertebrates. J. Mol. Evol. 37, 331-337.
7. Bernardi, G. (2000a). Isochores and the evolutionary genomics of vertebrates. Gene 241, 3-17.
8. Bernardi, G. (2000b). The compositional evolution of vertebrate genomes. Gene 241, 31-43.
9. Blaisdell, B. E. (1983). A prevalent persistent global nonrandomness that distinguishes coding from non-coding eucaryotic nuclear DNA sequences J. Mol. Evol. 19, 122-133.
10. Brendel, V., Beckmann, J. S. & Trifonov, E. N. (1986). Linguistics of nucleotide sequences: morphology and comparison of vocabularies. J. Biomol. Struct. Dyn. 4, 11-21.
11. Buldyrev, S. V., Goldberg, A. L., Havlin, S., Peng, C. K., Simons, M. & Stanley, H. E. (1993). Generalized Levy-Walk model for DNA nucleotide sequences. Phys. Rev. E 47, 4514-4523.
12. Burge, C., Campbell, A. M. & Karlin, S. (1992). Over-and under-representation of short oligonucleotides in DNA sequences. Proc. Natl Acad. Sci. U.S.A. 89, 1358-1362.
13. Clegg, M. T., Brandon, S. G., Learn, G. H. Jr & Morton, B. R. (1994). Rates and patterns of chloroplast DNA evolution. Proc. Natl Acad. Sci. U.S.A. 91, 6795-6801.
14. Duret, L., Mouchiroud, D. & Gautier, C. (1995). Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores. J. Mol. Evol. 40, 308-317.
15. Ebeling, W. & Nicolis, G. (1992). Word frequency and entropy in symbolic sequences: a dynamical perspective. Chaos Solitons Fractals 2, 635-650.
16. Francino, M. P. & Ochman, H. (1999). Isochores result from mutation not selection. Nature 400, 30-31.
17. Frugoli, J. A., Mcpeek, M. A., Thomas, T. L. & McClung, C. R. (1998). Intron loss and gain during evolution of the catalase gene family in angiosperms. Genetics 149, 355-365.
18. Gilbert, W., Marchionni, M. & McNight, G. (1986). On the antiquity of introns. Cell 46, 151-154.
19. Goffeau, A. et al. (1996). Life with 6000 genes. Science 274, 546-567.
20. Granero-Porati M. I. & Porati, A. (1988). Informational parameters and randomness of mitochondrial DNA. J. Mol. Evol. 27, 109-113.
21. Gray, M.W., Burger, G. & Lang, B.F. (1999). Mitochondrial evolution. Science 283, 1476-1481.
22. Gutiérrez, G., Oliver, J. L. & Marín, A. (1993). Dinucleotides and G+C content in human genes: Opposite behavior of GpG, GpC and TpC at II-III codon positions and in introns. J. Mol. Evol. 37, 131-136.
23. Hancock, J.M. & Armstrong, J. S. (1994). SIMPLE34: an improved and enhanced implementation for VAX and Sun computers of the SIMPLE algorithm for analysis of clustered repetitive motifs in nucleotide sequences. Comput. Appl. Biosci. 10, 67-70.
24. Herzel, H., Ebeling, W. & Schmitt, A. O. (1997). Entropies of biosequences: the role of repeats. Phys. Rev. E 50, 5061-5071.
25. Holmquist, G. P. (1989). Evolution of chromosomal bands: ecology of noncoding DNA. J. Mol. Evol. 28, 469-486.
26. Ikemura, T. & Wada, K. (1991). Evident diversity of codon usage patterns of human genes with respect to chromosome banding patterns and chromosome numbers; relation between nucleotide sequence data and cytogenetic data. Nucleic Acids Res. 19, 4333-4339.
27. Karlin, S. & Brendel, V. (1993). Patchiness and correlations in DNA sequences. Science 259, 677-680.
28. Karlin, S. & Ladunga, I. (1994). Comparison of eukaryotic genomic sequences. Proc. Natl Acad. Sci. U.S.A. 91, 12 832-12 836.
29. Kersanach, R., Brinkmann, H., Liaud, M. F., Zhang, D. X., Martin, W. & Cerff, R. (1994). Five identical intron positions in ancient duplicated genes of eubacterial origin. Nature 367, 387-389.
30. Knuth, D. E. (1981). The Art of Computer Programming. Reading, MA: Addison-Wesley Pub. Company.
31. Lewin, B. (1997). Genes VI. Oxford: Oxford University Press.
32. ́ spectrum in a noncoding DNA sequence. Europhys. Lett. 17, 655-660.
33. Peng, C. K., Buldyrev, S. V., Goldberger, A. L., Havlin, S., Sciortino, F., Simons, M. & Stanley, H. E. (1992) Long-range correlations in nucleotide sequences. Nature 356, 168-170.
34. Pietrokovski, S., Hirshon, J., Trifonov, E. N. (1990). Linguistic measure of taxonomic and functional relatedness of nucleotide sequences. J. Biomol. Struct. Dyn. 7, 1251-1268.
35. Poole, A. M., Jeffares, D. C. & Penny, D. (1998). The path from the RNA world. J. Mol. Biol. 46, 1-17.
36. Provata, A. & Almirantis, Y. (1997). Scaling properties of coding and non-coding DNA sequences. Physica A 247, 482-496.
37. Provata, A. & Almirantis, Y. (2000). Fractal Cantor patterns in the sequence structure of DNA. Fractals 8, 15-27.
38. Saccone, S., Federico, C., Solovei, I., Croquette, M. F., Della Valle, G. & Bernardi, G. (1999). Identification of the gene-richest bands in human prometaphase chromosomes. Chromosome Res. 7, 379-386.
39. Schnitzler, P., Hug, M., Handermann, M., Janssen, W., Koonin, E. V., Delius, H. & Darai, C. (1994a). Identification of genes encoding zinc finger proteins, non-histone chromosomal HMG protein homologue, and a putative GTP phosphohydrolase in the genome of Chilo iridescent virus. Nucleic Acids Res. 22, 158-166.
40. Schnitzler, P., Sonntag, K. C., Muller, M., Janssen, W., Bugert, J. J., Koonin, E. V. & Darai, G. (1994b). Insect iridescent virus type 6 encodes a polypeptide related to the largest subunit of eukaryotic RNA polymerase II. J. Gen. Virol. 75, 1557-1567.
41. Small, R. L. & Wentel, J. F. (2000). Copy number lability and evolutionary dynamics of the Adh gene family in diploid and tetraploid cotton (Gossypium). Genetics 155, 1913-1926.
42. Suzuki, Y. et al. (2001). Identification and characterization of the potential promoter regions of 1031 kinds of human genes. Genome Res. 11, 677.
43. Trifonov, E. N. (1989). The multiple codes of nucleotide sequences. Bull. Math. Biol. 51, 417-432.
44. Trifonov, E. N. (1990). Making sense of the human genome. In Human Genome Initiative and DNA Recombination (Sarma, R. H. & Sarma, M. H. eds), Vol. 1, pp. 329-338. Adenine Press.
45. Trifonov, E. N. & Sussman, J. L. (1980). The pitch of chromatine DNA is reflected in its nucleotide sequence. Proc. Natl Acad. Sci. U.S.A. 77, 3816-3820.
46. Voss, R. F. (1992). Evolution of long-range fractal correlations and 1/f noice in DNA base sequences. Phys. Rev. Lett. 68, 3805-3808.
47. Zhang, Q. M. (1998). Identification of human gene core promoters in silico. Genome Res. 8, 319-326.
48. Zuckerkandl, E. (1986). Polite DNA: functional density and functional compatibility in genomes. J. Mol. Evol. 24, 12-27.
49. Zuckerkandl, E. (1992). Revisiting junk DNA. J. Mol. Evol. 34, 259-271.