CorGen - Measuring and generating long-range correlations for DNA sequence analysis

Nucleic Acids Research

Volumn 34, Issue WEB. SERV. ISS., 2006, Pages

  Messer, Philipp W ^a   Arndt, Peter F ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; GUANINE;

ANALYTICAL PARAMETERS; ARTICLE; AUTOMATION; CORRELATION ANALYSIS; DNA CONTENT; DNA DETERMINATION; DNA SEQUENCE; EUKARYOTE; GENETIC ALGORITHM; GENETIC DATABASE; GENOME ANALYSIS; INTERNET; MATHEMATICAL COMPUTING; PRIORITY JOURNAL; PROTEIN CONTENT; PROTEIN DETERMINATION; PROTEIN MOTIF; SCORING SYSTEM; SEQUENCE ALIGNMENT; ALGORITHM; BIOLOGY; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; DNA BASE COMPOSITION; GENOMICS; HUMAN; METHODOLOGY; STATISTICAL ANALYSIS;

EUKARYOTA;

ALGORITHMS; BASE COMPOSITION; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; CYTOSINE; DATA INTERPRETATION, STATISTICAL; GENOMICS; GUANINE; HUMANS; INTERNET; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 33747843694     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl234     Document Type: Article

References (16)

1. Peng,C.-K., Buldyrev,S.V., Goldberger,A.L., Havlin,S., Sciortino,F., Simons,M. and Stanley,H.E. (1992) Long-range correlations in nucleotide sequences. Nature, 356, 168.
2. α spectrum in a noncoding DNA sequence. Europhys. Lett., 17, 655.
3. Voss,R.F. (1992) Evolution of long-range fractal correlations and 1/f noise in DNA base sequences. Phys. Rev. Lett., 68, 3805.
4. Arneodo,A., Bacry,E., Graves,P.V. and Muzy,J.F. (1995) Characterizing long-range correlations in DNA sequences from wavelet analysis. Phys. Rev. Lett., 74, 3293.
5. Bernaola-Galvan,P., Carpena,P., Roman-Roldan,R. and Oliver,J.L. (2002) Study of statistical correlations in DNA sequences. Gene, 300, 105.
6. Li,W. and Holste,D. (2005) Universal 1/f noise, crossovers of scaling exponents, and chromosome-specific patterns of guanine-cytosine content in DNA sequences of the human genome. Phys. Rev. E, 71, 041910.
7. Clay,O. and Bernardi,G. (2001) Compositional heterogeneity within and among isochores in mammalian genomes: II. Some general comments. Gene, 276, 25.
8. Durbin,R., Eddy,S., Krogh,A. and Mitchison,G. (1998) Biological Sequence Analysis. Cambridge University Press, Cambridge, England ISBN: 0-521-62971-3.
9. Messer,P.W., Arndt,P.F. and Lässig,M. (2005) Solvable sequence evolution models and genomic correlations. Phys. Rev. Lett., 94, 138103.
10. Messer,P.W., Bundschuh,R., Vingron,M. and Arndt,P.F. (2006) Alignment statistics for long-range correlated genomic sequences. In Apostolico, A., Guerra, C., Istrail, S., Pevzner, P.A. and Waterman, M.S. (eds), Proceedings of the Tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2006). Springer, Venice, Italy, pp. 426-440.
11. Tompa,M., Li,N., Bailey,T.L., Church,G.M., De Moor,B., Eskin,E., Favorov,A.V., Frith,M.C., Fu,Y. and Kent,W.J. (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol., 23, 137.
12. Makse,H.A., Havlin,S., Schwartz,M. and Stanley,H.E. (1996) Method for generating long-range correlations for large systems. Phys. Rev. E, 53, 5445.
13. Wang,X.J. (1989) Statistical physics of temporal intermittency. Phys. Rev. A, 40, 6647.
14. Clegg,R.G. and Dodson,M. (2005) Markov chain-based method for generating long-range dependence. Phys. Rev. E., 72, 026118.
15. Li,W. (1991) Expansion-modification systems: A model for spatial 1/f spectra. Phys. Rev. A, 43, 5240.
16. Messer,P.W., Lässig,M. and Arndt,P.F. (2005) Universality of long-range correlations in expansion-randomization systems. J. Stat. Mech, P10004.