Topological entropy of DNA sequences

Bioinformatics

Volumn 27, Issue 8, 2011, Pages 1061-1067

  Koslicki, David ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; CHEMISTRY; DNA SEQUENCE; ENTROPY; EXON; HUMAN; HUMAN GENOME; INTRON; Y CHROMOSOME;

CHROMOSOMES, HUMAN, Y; DNA; ENTROPY; EXONS; GENOME, HUMAN; HUMANS; INTRONS; SEQUENCE ANALYSIS, DNA;

EID: 79954465218     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr077     Document Type: Article

References (25)

1. Blanchard,F. et al. (eds) (2000) Topics in Symbolic Dynamics and Applications. London Mathematical Society Lecture Note Series 279. Cambridge University Press, Cambridge, UK.
2. Blankenberg,D. et al. (2007)Aframework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res., 17, 960-964.
3. Blankenberg,D. et al. (2010) Galaxy: a web-based genome analysis tool for experimentalists. Curr. Protocol. Mol. Biol., 19, 1-21.
4. Colosimo,A. and de Luca,A. (2000) Special factors in biological strings. J. Theor. Biol., 204, 29-46.
5. Crochemore,M. and Vèrin,R. (1999) Zones of low entropy in genomic sequences. Comput. Chem., 23, 275-282.
6. Farach,M. et al. (1995) On the entropy of DNA: algorithms and measurements based on memory and rapid convergence. In Proceedings of the sixth annual ACM-SIAM symposium on discrete algorithms. SIAM, Philadelphia, PA, pp. 48-57.
7. Gabrielian,A. and Bolshoy,A. (1999) Sequence complexity and DNA curvature. Computers & Chemistry, 23, 263-274.
8. Gheorghiciuc,I. and Ward,M.D. (2007) On correlation polynomials and subword complexity. In Conference on Analysis of Algorithms, Discrete Mathematics and Theoretical Computer Science Proceedings AH. Nancy, France, pp. 1-18.
9. Graves,J.A.M. (2006) Sex chromosome specialization and degeneration in mammals. Cell, 124, 901-914.
10. Hasegawa,M. et al. (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol., 22, 160-174.
11. Jukes,T.H. and Cantor,C.R. (1969) Evolution of protein molecules. In Munro,H.N. (ed.) Mammalian Protein Metabolism. Academic Press, New York, pp. 21-132.
12. Karamanos,K et al. (2006) Statistical compressibility analysis of DNA sequences by generalized entropy-like quantities: towards algorithmic laws for Biology? Proc. 6th WSEAS Int. Conf. Appl. Informat. Commun., 18, 481-491.
13. Kirillova,O.V. (2000) Entropy concepts and DNA investigations. Phys. Lett. A, 274, 247-253.
14. Larsson,N.J. (1999) Structures of String Matching and Data Compression. PhD Thesis, Lund University, Sweden.
15. Mantegna,R.N. et al. (1995) Systematic analysis of coding and noncoding DNA sequences using methods of statistical linguistics. Phys. Rev. E, 52, 2939-2950.
16. Ornstein,D. and Weiss,B. (2007) Entropy is the only finitely observable invariant. J. Mod. Dyn., 1, 93-107.
17. Rènyi,A. (1961) On measures of information and entropy. In Proceedings of the 4th Berkely Symposium on Mathematical Statistics and Probability, Vol. I. University of California Press, Berkely, CA, pp. 547-561.
18. Schmitt,A.O. and Herzel,H. (1997) Estimating the entropy of DNAsequences. J. Theor. Biol., 1888, 369-377.
19. Shannon,C.E. (1948) A Mathematical theory of communication. Bell Syst. Tech. J., 27, 379-423.
20. Siepel,A. et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res., 15, 1034-1050.
21. Stanley,H.E. (1999) Scaling features of noncoding DNA. Phys. A, 273, 1-18.
22. Troyanskaya,O.G. et al. (2002) Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity. Bioinformatics, 18, 679-688.
23. Vinga,S.andAlmeida,J.S. (2004)Rènyicontinuousentropyof DNAsequences.J.Theor. Biol., 231, 377-388.
24. Wilson,M.A. and Makova,K.D. (2009a) Genomic analyses of sex chromosome evolution. Annu. Rev. Genome Hum. Genet., 10, 333-354.
25. Wilson,M.A. and Makova,K.D. (2009b) Evolution and survival on eutherian sex chromosomes. PLoS, 5, e1000568.