메뉴 건너뛰기




Volumn 253, Issue 2, 2008, Pages 281-288

Data compression and genomes: A two-dimensional life domain map

Author keywords

Algorithms; DNA sequences; Evolutionary dynamics; Lempel Ziv compression; Statistical analysis

Indexed keywords

NUCLEOTIDE;

EID: 45649084526     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2008.03.011     Document Type: Article
Times cited : (12)

References (43)
  • 1
    • 45649084229 scopus 로고    scopus 로고
    • The biological meaning of DNA correlations
    • Losa G.A., Merlini D., Nonnenmacher T.F., and Weibel E.R. (Eds)
    • Acquisti C., Buiatti M., Mersi G., Bogani P., and Buiatti M. The biological meaning of DNA correlations. In: Losa G.A., Merlini D., Nonnenmacher T.F., and Weibel E.R. (Eds). Fractals in Biology and Medicine vol. 3 (2002) 235-247
    • (2002) Fractals in Biology and Medicine , vol.3 , pp. 235-247
    • Acquisti, C.1    Buiatti, M.2    Mersi, G.3    Bogani, P.4    Buiatti, M.5
  • 4
    • 0000003625 scopus 로고    scopus 로고
    • Non-Gaussian statistics of anomalous diffusion: the DNA sequences of prokaryotes
    • Allegrini P., Buiatti M., Grigolini P., and West B. Non-Gaussian statistics of anomalous diffusion: the DNA sequences of prokaryotes. Phys. Rev. E 58 (1998) 3640-3648
    • (1998) Phys. Rev. E , vol.58 , pp. 3640-3648
    • Allegrini, P.1    Buiatti, M.2    Grigolini, P.3    West, B.4
  • 10
    • 0043263931 scopus 로고    scopus 로고
    • Computational information for the logistic map at the chaos threshold
    • Bonanno C., and Menconi G. Computational information for the logistic map at the chaos threshold. Disc. Cont. Dyn. Syst.-B 2 3 (2002) 415-431
    • (2002) Disc. Cont. Dyn. Syst.-B , vol.2 , Issue.3 , pp. 415-431
    • Bonanno, C.1    Menconi, G.2
  • 11
    • 45649083478 scopus 로고    scopus 로고
    • Buiatti, M., 2006. Long range correlations in biological time series. Ph.D. Thesis, Paris VI.
    • Buiatti, M., 2006. Long range correlations in biological time series. Ph.D. Thesis, Paris VI.
  • 12
    • 0141990843 scopus 로고    scopus 로고
    • Towards a statistical characterization of the living state of matter
    • Buiatti M., and Buiatti M. Towards a statistical characterization of the living state of matter. Chaos Solitons and Fractals 20 (2004) 55-61
    • (2004) Chaos Solitons and Fractals , vol.20 , pp. 55-61
    • Buiatti, M.1    Buiatti, M.2
  • 13
    • 13444299064 scopus 로고    scopus 로고
    • The living state of matter: between noise and homeorrhetic constraints
    • Gell-Mann M., and Tsallis C. (Eds), Oxford University Press, Cambridge, MA
    • Buiatti M., Bogani P., Acquisti C., Mersi G., and Fronzoni L. The living state of matter: between noise and homeorrhetic constraints. In: Gell-Mann M., and Tsallis C. (Eds). Non Extensive Entropy: Inter-disciplinary Applications (2004), Oxford University Press, Cambridge, MA 221-241
    • (2004) Non Extensive Entropy: Inter-disciplinary Applications , pp. 221-241
    • Buiatti, M.1    Bogani, P.2    Acquisti, C.3    Mersi, G.4    Fronzoni, L.5
  • 16
    • 21044437200 scopus 로고    scopus 로고
    • Genome phylogeny based on short-range correlations in DNA sequences
    • Dehnert M., Plaumann R., Helm W.E., and Hutt M.T. Genome phylogeny based on short-range correlations in DNA sequences. J. Comput. Biol. 12 5 (2005) 545-553
    • (2005) J. Comput. Biol. , vol.12 , Issue.5 , pp. 545-553
    • Dehnert, M.1    Plaumann, R.2    Helm, W.E.3    Hutt, M.T.4
  • 17
    • 8844220452 scopus 로고    scopus 로고
    • STAR: an algorithm to search for tandem approximate repeats
    • Delgrange O., and Rivals E. STAR: an algorithm to search for tandem approximate repeats. Bioinformatics 20 16 (2004) 2812-2820
    • (2004) Bioinformatics , vol.20 , Issue.16 , pp. 2812-2820
    • Delgrange, O.1    Rivals, E.2
  • 18
    • 84925291641 scopus 로고    scopus 로고
    • Grumbach, S., Tahi, F., 1993. Compression of DNA sequences. Data Compression Conference 1993, 30 March-2 April 1993, pp. 340-350.
    • Grumbach, S., Tahi, F., 1993. Compression of DNA sequences. Data Compression Conference 1993, 30 March-2 April 1993, pp. 340-350.
  • 20
    • 19544369461 scopus 로고    scopus 로고
    • Hagenauer, J., Dawy, Z., Gobel, B., Hanus, P., Mueller, J., 2004. Genomic analysis using methods from information theory. IEEE Information Theory Workshop, 24-29 October 2004, pp. 55-59.
    • Hagenauer, J., Dawy, Z., Gobel, B., Hanus, P., Mueller, J., 2004. Genomic analysis using methods from information theory. IEEE Information Theory Workshop, 24-29 October 2004, pp. 55-59.
  • 21
    • 0032891716 scopus 로고    scopus 로고
    • 10-11 bp periodicities in complete genomes reflect protein structure and DNA folding
    • Herzel H., Weiss O., and Trifonov E.N. 10-11 bp periodicities in complete genomes reflect protein structure and DNA folding. Bioinformatics 15 3 (1999) 187-193
    • (1999) Bioinformatics , vol.15 , Issue.3 , pp. 187-193
    • Herzel, H.1    Weiss, O.2    Trifonov, E.N.3
  • 24
    • 0001494176 scopus 로고
    • On the entropy per time unit as a metric invariant of automorohism
    • Kolmogorov A.N. On the entropy per time unit as a metric invariant of automorohism. Dokl. Acad. Nauk. 124 (1959) 754-755
    • (1959) Dokl. Acad. Nauk. , vol.124 , pp. 754-755
    • Kolmogorov, A.N.1
  • 25
    • 0031298464 scopus 로고    scopus 로고
    • The study of correlation structures of DNA sequences: a critical review
    • Li W. The study of correlation structures of DNA sequences: a critical review. Comput. Chem. 21 4 (1997) 257-271
    • (1997) Comput. Chem. , vol.21 , Issue.4 , pp. 257-271
    • Li, W.1
  • 26
    • 84956088098 scopus 로고
    • Long-range correlation and partial 1/f-alpha spectrum in a non-coding DNA sequence
    • Li W., and Kaneko K. Long-range correlation and partial 1/f-alpha spectrum in a non-coding DNA sequence. Europhys. Lett. 17 7 (1992) 655-660
    • (1992) Europhys. Lett. , vol.17 , Issue.7 , pp. 655-660
    • Li, W.1    Kaneko, K.2
  • 28
    • 0035102453 scopus 로고    scopus 로고
    • An information based sequence distance and its application to whole mithocondrial genome phylogeny
    • Li M., Badger J.H., Chen X., Kwong S., Kearney P., and Zhang H. An information based sequence distance and its application to whole mithocondrial genome phylogeny. Bioinformatics 17 2 (2001) 149-154
    • (2001) Bioinformatics , vol.17 , Issue.2 , pp. 149-154
    • Li, M.1    Badger, J.H.2    Chen, X.3    Kwong, S.4    Kearney, P.5    Zhang, H.6
  • 29
    • 0028148067 scopus 로고
    • Third codon G + C periodicity as a possible signal for an internal selective constraint
    • Lió P., Ruffo S., and Buiatti M. Third codon G + C periodicity as a possible signal for an internal selective constraint. J. Theor. Biol. 171 2 (1994) 215-223
    • (1994) J. Theor. Biol. , vol.171 , Issue.2 , pp. 215-223
    • Lió, P.1    Ruffo, S.2    Buiatti, M.3
  • 30
    • 39049189269 scopus 로고    scopus 로고
    • A compression-based approach for coding sequences identification I. Prokaryotic genomes
    • Menconi G., and Marangoni R. A compression-based approach for coding sequences identification I. Prokaryotic genomes. J. Comput. Biol. 13 8 (2006)
    • (2006) J. Comput. Biol. , vol.13 , Issue.8
    • Menconi, G.1    Marangoni, R.2
  • 31
    • 0033609333 scopus 로고    scopus 로고
    • Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima
    • Nelson K.E., et al. Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima. Nature 399 (1999) 323-329
    • (1999) Nature , vol.399 , pp. 323-329
    • Nelson, K.E.1
  • 32
    • 3242892432 scopus 로고    scopus 로고
    • Complexity: an internet resource for analysis of DNA sequence complexity
    • Orlov Y.L., and Potapov V.N. Complexity: an internet resource for analysis of DNA sequence complexity. Nucl. Acids Res. 32 (2004) W628-W633
    • (2004) Nucl. Acids Res. , vol.32
    • Orlov, Y.L.1    Potapov, V.N.2
  • 33
    • 0242643741 scopus 로고    scopus 로고
    • A new sequence distance measure for phylogenetic tree construction
    • Otu H.H., and Sayood K. A new sequence distance measure for phylogenetic tree construction. Bioinformatics 19 16 (2003) 2122-2130
    • (2003) Bioinformatics , vol.19 , Issue.16 , pp. 2122-2130
    • Otu, H.H.1    Sayood, K.2
  • 34
    • 0031351245 scopus 로고    scopus 로고
    • Scaling properties of coding and non-coding DNA sequences
    • Provata A., and Almirantis Y. Scaling properties of coding and non-coding DNA sequences. Physica A 247 (1997) 482-496
    • (1997) Physica A , vol.247 , pp. 482-496
    • Provata, A.1    Almirantis, Y.2
  • 35
    • 2442476580 scopus 로고    scopus 로고
    • The mammalian transcriptome and the function of non-coding DNA sequences
    • Shabalina S.A., and Spiridonov N.A.S. The mammalian transcriptome and the function of non-coding DNA sequences. Genome Biol. 5 (2004) 105
    • (2004) Genome Biol. , vol.5 , pp. 105
    • Shabalina, S.A.1    Spiridonov, N.A.S.2
  • 36
    • 34748835079 scopus 로고    scopus 로고
    • Szpankowski, W., Ren, W., Szpankowski, L., 2003. An optimal DNA segmentation based on the MDL principle. In: Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003, 11-14 August 2003, pp. 541-546.
    • Szpankowski, W., Ren, W., Szpankowski, L., 2003. An optimal DNA segmentation based on the MDL principle. In: Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003, 11-14 August 2003, pp. 541-546.
  • 37
    • 0024334889 scopus 로고    scopus 로고
    • Trifonov, E.N., 1989. The multiple codes of nucleotide sequences. Bull. Math. Biol. 417-432.
    • Trifonov, E.N., 1989. The multiple codes of nucleotide sequences. Bull. Math. Biol. 417-432.
  • 38
    • 0000204878 scopus 로고
    • Evolution of long-range fractal correlations and 1/f noise in DNA-base sequences
    • Voss R.F. Evolution of long-range fractal correlations and 1/f noise in DNA-base sequences. Phys. Rev. Lett. 68 25 (1992) 3805-3808
    • (1992) Phys. Rev. Lett. , vol.68 , Issue.25 , pp. 3805-3808
    • Voss, R.F.1
  • 39
    • 0015997746 scopus 로고
    • A catastrophe theory of evolution
    • Waddington C.H. A catastrophe theory of evolution. Ann. NY Acad. Sci. 231 (1975) 32-42
    • (1975) Ann. NY Acad. Sci. , vol.231 , pp. 32-42
    • Waddington, C.H.1
  • 40
    • 0034141421 scopus 로고    scopus 로고
    • Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima
    • Worning P., Jensen L.J., Nelson K.E., Brunak S., and Ussery D.W. Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima. Nucl. Acids Res. 28 3 (2000) 706-709
    • (2000) Nucl. Acids Res. , vol.28 , Issue.3 , pp. 706-709
    • Worning, P.1    Jensen, L.J.2    Nelson, K.E.3    Brunak, S.4    Ussery, D.W.5
  • 41
    • 33751181225 scopus 로고    scopus 로고
    • Xia, C., Ooi, B.C., Tung, A.K.H., Pang, H.H., Tan, K.-L., 2005. DSIM: a distance-based indexing method for genomic sequences. Fifth IEEE Symposium on Bioinformatics and Bioengineering, 2005. BIBE 2005 19-21 October 2005, pp. 97-104.
    • Xia, C., Ooi, B.C., Tung, A.K.H., Pang, H.H., Tan, K.-L., 2005. DSIM: a distance-based indexing method for genomic sequences. Fifth IEEE Symposium on Bioinformatics and Bioengineering, 2005. BIBE 2005 19-21 October 2005, pp. 97-104.
  • 42
    • 0017493286 scopus 로고
    • A universal algorithm for sequential data compression
    • Ziv J., and Lempel A. A universal algorithm for sequential data compression. IEEE Trans. Inf. Theory 23 (1977) 337-342
    • (1977) IEEE Trans. Inf. Theory , vol.23 , pp. 337-342
    • Ziv, J.1    Lempel, A.2
  • 43
    • 0018019231 scopus 로고
    • Compression of individual sequences via variable-rate coding
    • Ziv J., and Lempel A. Compression of individual sequences via variable-rate coding. IEEE Trans. Inf. Theory 24 (1978) 530-536
    • (1978) IEEE Trans. Inf. Theory , vol.24 , pp. 530-536
    • Ziv, J.1    Lempel, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.