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Volumn 6, Issue 1-2, 2006, Pages 71-78

DNA motifs and sequence periodicities

Author keywords

C. elegans; Correlation; DNA bendability; Genomic DNA; Motif; Nucleosomes; Periodicities; Poly(A) sequences; Supercoiling

Indexed keywords

CURVED DNA; DNA BINDING PROTEIN; GENOMIC DNA; TETRAMER;

EID: 33745222322     PISSN: 13866338     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article
Times cited : (21)

References (27)
  • 2
    • 11344252296 scopus 로고    scopus 로고
    • DNA Bendability and Nucleosome Positioning in Transcriptional Regulation
    • Takashi Ohyaman (ed.), Eurekah Bioscience Database, chapter 14
    • Dlakic, M., Ussery, D. W. and Brunak, S. (2004). DNA Bendability and Nucleosome Positioning in Transcriptional Regulation. In: DNA Conformation and Transcription, Takashi Ohyaman (ed.), Eurekah Bioscience Database, chapter 14, pp. 1-14.
    • (2004) DNA Conformation and Transcription , pp. 1-14
    • Dlakic, M.1    Ussery, D.W.2    Brunak, S.3
  • 4
    • 0028624664 scopus 로고
    • Bending and curvature calculations in B-DNA
    • Goodsell, D. S. and Dickerson, R. E. (1994). Bending and curvature calculations in B-DNA. Nucleic Acids Res. 22, 5497-5503.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 5497-5503
    • Goodsell, D.S.1    Dickerson, R.E.2
  • 5
    • 0842346757 scopus 로고    scopus 로고
    • Seven clusters in genomic triplet distributions
    • Gorban, A., Zinovyev, A. Y. and Popova, T. G. (2003). Seven clusters in genomic triplet distributions. In Silico Biol. 3, 0039.
    • (2003) In Silico Biol. , vol.3 , pp. 0039
    • Gorban, A.1    Zinovyev, A.Y.2    Popova, T.G.3
  • 6
    • 0028073817 scopus 로고
    • Sequence elements responsible for DNA curvature
    • Haran, T. E., Kahn, J. D. and Crothers, D. M. (1994). Sequence elements responsible for DNA curvature. Mol. Biol. 244, 135-143.
    • (1994) Mol. Biol. , vol.244 , pp. 135-143
    • Haran, T.E.1    Kahn, J.D.2    Crothers, D.M.3
  • 7
    • 0031757877 scopus 로고    scopus 로고
    • Sequence periodicity in complete genomes of archaea suggests positive supercoiling
    • Herzel, H., Weiss, O. and Trifonov, E. N. (1998). Sequence periodicity in complete genomes of archaea suggests positive supercoiling. J. Biomol. Struct. Dyn. 16, 341-345.
    • (1998) J. Biomol. Struct. Dyn. , vol.16 , pp. 341-345
    • Herzel, H.1    Weiss, O.2    Trifonov, E.N.3
  • 8
    • 0032891716 scopus 로고    scopus 로고
    • 10-11 by periodicities in complete genomes reflect protein structure and DNA folding
    • Herzel, H., Weiss, O. and Trifonov, E. N. (1999). 10-11 by periodicities in complete genomes reflect protein structure and DNA folding. Bioinformatics 15, 187-193.
    • (1999) Bioinformatics , vol.15 , pp. 187-193
    • Herzel, H.1    Weiss, O.2    Trifonov, E.N.3
  • 9
    • 0034699776 scopus 로고    scopus 로고
    • Optimization of coding potentials using positional dependence of nucleotide frequencies
    • Holste, D., Grosse, I., Buldyrev, S. V., Stanley, H. E. and Herzel, H. (2000). Optimization of coding potentials using positional dependence of nucleotide frequencies. J. Theor. Biol. 206, 525-537.
    • (2000) J. Theor. Biol. , vol.206 , pp. 525-537
    • Holste, D.1    Grosse, I.2    Buldyrev, S.V.3    Stanley, H.E.4    Herzel, H.5
  • 11
    • 0030595138 scopus 로고    scopus 로고
    • Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences
    • Ioshikhes, I., Bolshoy, A., Derenshteyn, K., Borodovsky, M. and Trifonov, E. N. (1996). Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences. J. Mol. Biol. 262, 129-139.
    • (1996) J. Mol. Biol. , vol.262 , pp. 129-139
    • Ioshikhes, I.1    Bolshoy, A.2    Derenshteyn, K.3    Borodovsky, M.4    Trifonov, E.N.5
  • 12
    • 0028956546 scopus 로고
    • Properties of a general model of DNA evolution under no-strand-bias conditions
    • Lobry, J. R. (1995). Properties of a general model of DNA evolution under no-strand-bias conditions. J. Mol. Evol. 40, 326-330.
    • (1995) J. Mol. Evol. , vol.40 , pp. 326-330
    • Lobry, J.R.1
  • 13
    • 0034660586 scopus 로고    scopus 로고
    • The global intrinsic curvature of archael and eubacterial genomes is mostly contained in their dinucleotide composition and is probably not an adaptation
    • Merino, E. and Garciarrubio, A. (2000). The global intrinsic curvature of archael and eubacterial genomes is mostly contained in their dinucleotide composition and is probably not an adaptation. Nucleic Acids Res. 28, 2431-2438.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 2431-2438
    • Merino, E.1    Garciarrubio, A.2
  • 14
    • 0000541574 scopus 로고    scopus 로고
    • Twenty Years of DNA Bending
    • R. H. Sarma and M. H. Sarma (eds.), Adenine Press
    • Olson, W. K. and Zhurkin, V. B. (1996). Twenty Years of DNA Bending. In: Biological Structure and Dynamics, R. H. Sarma and M. H. Sarma (eds.), Adenine Press, pp. 341-370.
    • (1996) Biological Structure and Dynamics , pp. 341-370
    • Olson, W.K.1    Zhurkin, V.B.2
  • 15
    • 0023001414 scopus 로고
    • Sequence periodicities in chicken nucleosome core DNA
    • Satchwell, S. C., Drew, H. R. and Travers, A. A. (1986). Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol. 191, 659-675.
    • (1986) J. Mol. Biol. , vol.191 , pp. 659-675
    • Satchwell, S.C.1    Drew, H.R.2    Travers, A.A.3
  • 16
    • 5144227142 scopus 로고    scopus 로고
    • Periodicities of 10-11 bp as indicators of the supercoiled state of genomic DNA
    • Schieg, P. and Herzel, H. (2004). Periodicities of 10-11 bp as indicators of the supercoiled state of genomic DNA. J. Mol. Biol. 343, 891-901.
    • (2004) J. Mol. Biol. , vol.343 , pp. 891-901
    • Schieg, P.1    Herzel, H.2
  • 17
    • 0023650543 scopus 로고
    • The codon Adaptation Index - A measure of directional synonymous codon usage bias, and its potential application
    • Sharp, P. M. and Li, W.-H. (1987). The codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential application. Nucleic Acids Res. 15, 1281-1295.
    • (1987) Nucleic Acids Res. , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.-H.2
  • 18
    • 0001079085 scopus 로고
    • Artificial nucleosome positioning sequences
    • Shrader, T. E. and Crothers, D. M. (1989). Artificial nucleosome positioning sequences. Proc. Natl. Acad. Sci. USA 86, 7418-7422.
    • (1989) Proc. Natl. Acad. Sci. USA , vol.86 , pp. 7418-7422
    • Shrader, T.E.1    Crothers, D.M.2
  • 19
    • 0039837085 scopus 로고    scopus 로고
    • Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences
    • Thastrom, A., Lowary, P. T., Widlund, H. R., Cao, H., Kubista, M. and Widom, J. (1999). Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences. J. Mol. Biol. 288, 213-229.
    • (1999) J. Mol. Biol. , vol.288 , pp. 213-229
    • Thastrom, A.1    Lowary, P.T.2    Widlund, H.R.3    Cao, H.4    Kubista M. Widom, J.5
  • 20
    • 0032770571 scopus 로고    scopus 로고
    • ApA dinucleotide periodicity in prokaryote, eukaryote, and organelle genomes
    • Tomita, M., Wada, M. and Kawashima, Y. (1999). ApA dinucleotide periodicity in prokaryote, eukaryote, and organelle genomes. J. Mol. Evol. 49, 182-192.
    • (1999) J. Mol. Evol. , vol.49 , pp. 182-192
    • Tomita, M.1    Wada, M.2    Kawashima, Y.3
  • 21
    • 0025069835 scopus 로고
    • Why bend DNA?
    • Travers, A. A. (1990). Why bend DNA? Cell 60, 177-180.
    • (1990) Cell , vol.60 , pp. 177-180
    • Travers, A.A.1
  • 22
    • 0001415964 scopus 로고
    • The pitch of chromatin DNA is reflected in its nucleotide sequence
    • Trifonov, E. N. and Sussman, J. L. (1980). The pitch of chromatin DNA is reflected in its nucleotide sequence. Proc. Natl. Acad. Sci. USA 77, 3816-3820.
    • (1980) Proc. Natl. Acad. Sci. USA , vol.77 , pp. 3816-3820
    • Trifonov, E.N.1    Sussman, J.L.2
  • 23
    • 0032554318 scopus 로고    scopus 로고
    • Correlations in protein sequences and property codes
    • Weiss, O. and Herzel, H. (1998). Correlations in protein sequences and property codes. J. theor. Biol. 190, 341-353.
    • (1998) J. Theor. Biol. , vol.190 , pp. 341-353
    • Weiss, O.1    Herzel, H.2
  • 24
    • 0030596486 scopus 로고    scopus 로고
    • Short-range order in two eukaryotic genomes: Relation to chromosome structure
    • Widom, J. (1996). Short-range order in two eukaryotic genomes: Relation to chromosome structure. J. Mol. Biol. 259, 579-588.
    • (1996) J. Mol. Biol. , vol.259 , pp. 579-588
    • Widom, J.1
  • 26
    • 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. (2000). Structural analysis of DNA sequence: Evidence for lateral gene transfer in Thermotoga maritima. Nucleic Acids Res. 28, 706-709.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 706-709
    • Worning, P.1    Jensen, L.J.2    Nelson, K.E.3    Brunak, S.4    Ussery, D.W.5
  • 27
    • 0019887286 scopus 로고
    • Periodicity in DNA primary structure is defined by secondary structure of the coded protein
    • Zhurkin, V. B. (1981). Periodicity in DNA primary structure is defined by secondary structure of the coded protein. Nucleic Acids Res. 9, 1963-1971.
    • (1981) Nucleic Acids Res. , vol.9 , pp. 1963-1971
    • Zhurkin, V.B.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.