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Mot-clé: linguistics of DNA sequences

[1] Beckmann, J. S., Brendel, V., and Trifonov, E. N. Intervening sequences exhibit distinct vocabulary. J. Biomol. Struct. Dynamics 4 (1986), 391-400.

[2] Brendel, V., Beckmann, J. S., and Trifonov, E. N. Linguistics of nucleotide sequences : Morphology and comparison of vocabularies. J. Biomol. Struct. Dynamics 4 (1986), 11-21.

[3] Burge, C., Campbell, A., and Karlin, S. Over- and under-representation of short oligonucleotides in DNA sequences. Proc. Natl. Acad. Sci. USA 89 (1992), 1358-1362.

[4] Cowan, R. Expected frequencies of DNA patterns using Whittle's formula. J. Appl. Prob. 28 (1991), 886-892.

[5] Karlin, S., Burge, C., and Campbell, A. M. Statistical analyses of counts and distributions of restriction sites in DNA sequences. Nucl. Acids Res. 20 (1992), 1363-1370.

[6] Nussinov, R. The universal dinucleotide asymmetry rules in DNA and the amino acid codon choice. J. Mol. Evol 17 (1981), 237-244.

[7] Pevzner, P. A., Borodovsky, M. Y., and Mironov, A. A. Linguistics of nucleotides sequences I: The significance of deviations from mean statistical characteristics and prediction of the frequencies of occurrence of words. J. Biomol. Struct. Dynamics 6 (1989), 1013-1026.

[8] Pevzner, P. A., Borodovsky, M. Y., and Mironov, A. A. Linguistics of nucleotides sequences II: Stationary words in genetic texts and the zonal structure of DNA. J. Biomol. Struct. Dynamics 6 (1989), 1027-1038.

[9] Phillips, G. J., Arnold, J., and Ivarie, R. The effect of codon usage on the oligonucleotide composition of the e. coli genome and identification of over- and underrepresented sequences by Markov chain analysis. Nucl. Acids Res. 15 (1987), 2627-2638.

[10] Phillips, G. J., Arnold, J., and Ivarie, R. Mono- through hexanucleotide composition of the escherichia coli genome : a Markov chain analysis. Nucl. Acids Res. 15 (1987), 2611-2626.

[11] Pietrokovski, S., and Trifonov, E. N. Imported sequences in the mitochondrial yeast genome identified by nucleotide linguistics. Gene 122 (1992), 129-137.

[12] Pietrokovsky, S., Hirshon, J., and Trifonov, E. N. Linguistic measure of taxonomic and functional relatedness of nucleotides sequences. J. Biomol. Struct. Dynamics 7 (1990), 1251-1268.

[13] Rocha, E., Viari, A., and Danchin, A. Oligonucleotide bias in Bacillus subtilis: general trends and taxonomic comparisons. Nucl. Acids Res. 26 (1998), 2971-2980.

[14] Schbath, S. Étude asymptotique du nombre d'occurrences d'un mot dans une chaîne de Markov et application à la recherche de mots de fréquence exceptionnelle dans les séquences d'ADN. PhD thesis, Université René Descartes, Paris V, 1995.

[15] Schbath, S. An efficient statistic to detect over- and under-represented words in DNA sequences. J. Comp. Biol. 4 (1997), 189-192.

[16] Schbath, S., Prum, B., and Turckheim, E. d. Exceptional motifs in different Markov chain models for a statistical analysis of DNA sequences. J. Comp. Biol. 2 (1995), 417-437.

[17] Stuckle, E. E., Emmrich, C., Grob, U., and Nielsen, P. J. Statistical analysis of nucleotide sequences. Nucl. Acids Res. 18 (1990), 6641-6647.

[18] Yomo, T., and Ohno, S. Concordant evolution of coding and noncoding regions of DNA made possible by the universal rule of TA/CG deficiency-TG/CT excess. Proc. Natl. Acad. Sci. USA 86 (1989), 8452-8456.

Fri Feb 11 09:39:23 MET 2000

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