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Volumn 9, Issue , 2008, Pages

The average mutual information profile as a genomic signature

Author keywords

[No Author keywords available]

Indexed keywords

AVERAGE MUTUAL INFORMATION; COMPUTATIONALLY EFFICIENT; EVOLUTIONARY ASPECTS; EVOLUTIONARY RELATIONSHIPS; MICROBIAL COMMUNITIES; ORGANIZATIONAL STRUCTURES; RAPID IDENTIFICATION; SPECIES SPECIFICS;

EID: 41549106766     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-48     Document Type: Article
Times cited : (43)

References (43)
  • 1
    • 0022592245 scopus 로고
    • A Simple Way to Look at DNA
    • 10.1016/S0022-5193(86)80144-8 3016414
    • Gates M A Simple Way to Look at DNA J Theor Biol 1986, 119:319-328. 10.1016/S0022-5193(86)80144-8 3016414
    • (1986) J Theor Biol , vol.119 , pp. 319-328
    • Gates, M.1
  • 2
    • 0000204878 scopus 로고
    • Evolution of long-range Fractal Correlations and 1/f Noise in DNA Base Sequences
    • 10.1103/PhysRevLett.68.3805
    • Voss R Evolution of long-range Fractal Correlations and 1/f Noise in DNA Base Sequences Phys Rev Letters 1992, 68(25):3805-3808. 10.1103/ PhysRevLett.68.3805
    • (1992) Phys Rev Letters , vol.68 , Issue.25 , pp. 3805-3808
    • Voss, R.1
  • 4
    • 0027621772 scopus 로고
    • Generalized Levy-Walk Model for DNA Nucleotide Sequences
    • 10.1103/PhysRevE.47.4514
    • Buldyrev S Goldberger A Havlin A Peng C Simons M Stanley H Generalized Levy-Walk Model for DNA Nucleotide Sequences Phys Rev E 1992, 47(6):4514-4523. 10.1103/PhysRevE.47.4514
    • (1992) Phys Rev E , vol.47 , Issue.6 , pp. 4514-4523
    • Buldyrev, S.1    Goldberger, A.2    Havlin, A.3    Peng, C.4    Simons, M.5    Stanley, H.6
  • 5
    • 0001503951 scopus 로고
    • Dynamical Walk Model for DNA Sequences
    • Allegrini P Barbi M Grigolini P West B Dynamical Walk Model for DNA Sequences Phys Rev E 1995 52 5 5281 5296 10.1103/PhysRevE.52.5281
    • (1995) Phys Rev E , vol.52 , pp. 5281-5296
    • Allegrini, P.1    Barbi, M.2    Grigolini, P.3    West, B.4
  • 7
    • 0030196610 scopus 로고    scopus 로고
    • Application of Information Theory to DNA Sequence Analysis: A Review
    • 10.1016/0031-3203(95)00145-X
    • Roman-Roldan R Bernaolo-Galvan P Oliver J Application of Information Theory to DNA Sequence Analysis: A Review Pattern Recognition 1996, 29(7):1187-1194. 10.1016/0031-3203(95)00145-X
    • (1996) Pattern Recognition , vol.29 , Issue.7 , pp. 1187-1194
    • Roman-Roldan, R.1    Bernaolo-Galvan, P.2    Oliver, J.3
  • 8
    • 0023042012 scopus 로고
    • Information Content of Binding Sites on Nucleotide Sequences
    • 10.1016/0022-2836(86)90165-8 3525846
    • Gold TSGSL Ehrefeucht A Information Content of Binding Sites on Nucleotide Sequences J Mol Biol 1986, 188:415-431. 10.1016/ 0022-2836(86)90165-8 3525846
    • (1986) J Mol Biol , vol.188 , pp. 415-431
    • Gold, T.S.G.S.L.1    Ehrefeucht, A.2
  • 9
    • 0025008168 scopus 로고
    • Sequence Logos: A New Way to Display Consensus Sequences
    • 332411 2172928 10.1093/nar/18.20.6097
    • Schneider T Stephens R Sequence Logos: A New Way to Display Consensus Sequences Nucleic Acid Res 1990, 18:6097-6100. 332411 2172928 10.1093/ nar/18.20.6097
    • (1990) Nucleic Acid Res , vol.18 , pp. 6097-6100
    • Schneider, T.1    Stephens, R.2
  • 10
    • 0000931192 scopus 로고    scopus 로고
    • Fast Multiple Alignment of Ungapped DNA Sequences Using Information Theory and a Relaxation Method
    • 10.1016/S0166-218X(96)00068-6
    • Schneider T Mastronade D Fast Multiple Alignment of Ungapped DNA Sequences Using Information Theory and a Relaxation Method Discrete Applied Mathematics 1996, 71:259-268. 10.1016/S0166-218X(96)00068-6
    • (1996) Discrete Applied Mathematics , vol.71 , pp. 259-268
    • Schneider, T.1    Mastronade, D.2
  • 11
    • 0342908877 scopus 로고    scopus 로고
    • Analysis of Correlations Between Sites in Models of Protein Sequences
    • 10.1103/PhysRevE.58.6312
    • Giraud B Lapedes A Liu L Analysis of Correlations Between Sites in Models of Protein Sequences Phys Rev E 1998, 58(5):6312-6322. 10.1103/ PhysRevE.58.6312
    • (1998) Phys Rev E , vol.58 , Issue.5 , pp. 6312-6322
    • Giraud, B.1    Lapedes, A.2    Liu, L.3
  • 12
    • 5244285298 scopus 로고    scopus 로고
    • Correlations in DNA Sequences: The Role of Protein Coding Segments
    • 10.1103/PhysRevE.55.800
    • Herzel H Grosse I Correlations in DNA Sequences: The Role of Protein Coding Segments Phys Rev E 1997, 55:800-810. 10.1103/PhysRevE.55.800
    • (1997) Phys Rev E , vol.55 , pp. 800-810
    • Herzel, H.1    Grosse, I.2
  • 13
    • 0027297096 scopus 로고
    • Covariation of Mutations in the V3 Loop of Human Immunodeficiency Virus Type I Envelope Protein: An Information Theoretic Analysis
    • 47099 8346232 10.1073/pnas.90.15.7176
    • Korber B Farber R Wolpert D Lapedes A Covariation of Mutations in the V3 Loop of Human Immunodeficiency Virus Type I Envelope Protein: An Information Theoretic Analysis Proc Natl Acad Sci 1993, 90:7176-7180. 47099 8346232 10.1073/pnas.90.15.7176
    • (1993) Proc Natl Acad Sci , vol.90 , pp. 7176-7180
    • Korber, B.1    Farber, R.2    Wolpert, D.3    Lapedes, A.4
  • 14
    • 0001366379 scopus 로고    scopus 로고
    • Statistical Correlation of Nucleotides in a DNA Sequence
    • 10.1103/PhysRevE.58.861
    • Luo L Lee W Statistical Correlation of Nucleotides in a DNA Sequence Phys Rev E 1998, 58:861-871. 10.1103/PhysRevE.58.861
    • (1998) Phys Rev E , vol.58 , pp. 861-871
    • Luo, L.1    Lee, W.2
  • 15
    • 0000387692 scopus 로고    scopus 로고
    • Sequence Compositional Complexity of DNA through an Entropic Segmentation Method
    • 10.1103/PhysRevLett.80.1344
    • Roman-Roldan R Bernaolo-Galvan P Oliver J Sequence Compositional Complexity of DNA through an Entropic Segmentation Method Phys Rev Letters 1999, 80(6):1344-1347. 10.1103/PhysRevLett.80.1344
    • (1999) Phys Rev Letters , vol.80 , Issue.6 , pp. 1344-1347
    • Roman-Roldan, R.1    Bernaolo-Galvan, P.2    Oliver, J.3
  • 16
    • 0000460109 scopus 로고    scopus 로고
    • Decomposition of DNA Sequence Complexity
    • 10.1103/PhysRevLett.83.3336
    • Bernaolo-Galvan P Oliver J Ramon-Roldan R Decomposition of DNA Sequence Complexity Phys Rev Letters 1999:3336-3339. 10.1103/PhysRevLett.83.3336
    • (1999) Phys Rev Letters , pp. 3336-3339
    • Bernaolo-Galvan, P.1    Oliver, J.2    Ramon-Roldan, R.3
  • 17
    • 0028028028 scopus 로고
    • Computational DNA Sequence Analysis
    • 10.1146/annurev.micro.48.1.619 7826021
    • Cardon SKL Computational DNA Sequence Analysis Annu Rev Microbiol 1994, 48:619-654. 10.1146/annurev.micro.48.1.619 7826021
    • (1994) Annu Rev Microbiol , vol.48 , pp. 619-654
    • Cardon, S.K.L.1
  • 18
    • 0027958329 scopus 로고
    • Molecular Evolution of Herpesviruses: Genomic and Protein Sequence Comparisons
    • 236651 8107249
    • Karlin S Mocarski E Schachtel G Molecular Evolution of Herpesviruses: Genomic and Protein Sequence Comparisons J Virol 1994, 68(3):1886-1902. 236651 8107249
    • (1994) J Virol , vol.68 , Issue.3 , pp. 1886-1902
    • Karlin, S.1    Mocarski, E.2    Schachtel, G.3
  • 19
    • 0029117163 scopus 로고
    • Statistical Significance of Sequence Patterns in Proteins
    • 10.1016/0959-440X(95)80098-0 7583634
    • Karlin S Statistical Significance of Sequence Patterns in Proteins Curr Opin Struct Biol 1995, 5(3):360-371. 10.1016/0959-440X(95)80098-0 7583634
    • (1995) Curr Opin Struct Biol , vol.5 , Issue.3 , pp. 360-371
    • Karlin, S.1
  • 20
    • 0030014818 scopus 로고    scopus 로고
    • Similarities and Dissimilarities of Phage Genomes
    • 39151 8650182 10.1073/pnas.93.12.5854
    • Blaisdell B Campbell A Karlin S Similarities and Dissimilarities of Phage Genomes Proc Natl Acad Sci USA 1996, 93(12):5854-5859. 39151 8650182 10.1073/pnas.93.12.5854
    • (1996) Proc Natl Acad Sci USA , vol.93 , Issue.12 , pp. 5854-5859
    • Blaisdell, B.1    Campbell, A.2    Karlin, S.3
  • 21
    • 1842332701 scopus 로고    scopus 로고
    • Compositional Biases of Bacterial Genomes and Evolutionary Implications
    • 179198 9190805
    • Karlin S Mrazek J Campbell A Compositional Biases of Bacterial Genomes and Evolutionary Implications J Bacteriol 1997, 179(12):3899-3913. 179198 9190805
    • (1997) J Bacteriol , vol.179 , Issue.12 , pp. 3899-3913
    • Karlin, S.1    Mrazek, J.2    Campbell, A.3
  • 22
    • 0022757813 scopus 로고
    • Linguistics of Nucleotide Sequences: Morphology and Comparison of Vocabularies
    • 3078230
    • Brendel V Beckmann J Trifonov E Linguistics of Nucleotide Sequences: Morphology and Comparison of Vocabularies J Biomol Struct Dyn 1986, 4:11-21. 3078230
    • (1986) J Biomol Struct Dyn , vol.4 , pp. 11-21
    • Brendel, V.1    Beckmann, J.2    Trifonov, E.3
  • 23
    • 0022854407 scopus 로고
    • Intervening Sequences Exhibit Distinct Vocabulary
    • 2482751
    • Beckmann J Brendel V Trifonov E Intervening Sequences Exhibit Distinct Vocabulary J Biomol Struct Dyn 1986, 4(3):391-400. 2482751
    • (1986) J Biomol Struct Dyn , vol.4 , Issue.3 , pp. 391-400
    • Beckmann, J.1    Brendel, V.2    Trifonov, E.3
  • 24
    • 0037472766 scopus 로고    scopus 로고
    • Pentamer Vocabularies Characterizing Introns and Intron-like Intergenic Tracts from Caenorhabditis elegans and Drosophila melanogaster
    • 10.1016/S0378-1119(02)01206-4 12568727
    • E EB Pizzi E Giudice PD Frontali C Pentamer Vocabularies Characterizing Introns and Intron-like Intergenic Tracts from Caenorhabditis elegans and Drosophila melanogaster Gene 2003, 304:183-192. 10.1016/ S0378-1119(02)01206-4 12568727
    • (2003) Gene , vol.304 , pp. 183-192
    • E, E.B.1    Pizzi, E.2    Giudice, P.D.3    Frontali, C.4
  • 25
    • 19744383764 scopus 로고    scopus 로고
    • Detection and Characterization of Horizontal Transfers in Prokaryotes Using Genomic Signature
    • 10.1093/nar/gni004
    • Dufraigne C Fertil B Lespinats S Giron A Deschavanne P Detection and Characterization of Horizontal Transfers in Prokaryotes Using Genomic Signature Nuc Acids Res 2005, 33:e6. 10.1093/nar/gni004
    • (2005) Nuc Acids Res , vol.33
    • Dufraigne, C.1    Fertil, B.2    Lespinats, S.3    Giron, A.4    Deschavanne, P.5
  • 28
    • 0029060923 scopus 로고
    • Dinucleotide Relative Abundance Extremes: A Genomic Signature
    • 10.1016/S0168-9525(00)89076-9 7482779
    • Karlin S Burge C Dinucleotide Relative Abundance Extremes: A Genomic Signature Trends Genet 1995, 11:283-290. 10.1016/S0168-9525(00)89076-9 7482779
    • (1995) Trends Genet , vol.11 , pp. 283-290
    • Karlin, S.1    Burge, C.2
  • 29
    • 0032823783 scopus 로고    scopus 로고
    • Genomic Signature: Characterization and Classification of Species Assessed by Chaos Game Representation of Sequences
    • Deschavanne P Giron A Vilain J Fagot G Fertil B Genomic Signature: Characterization and Classification of Species Assessed by Chaos Game Representation of Sequences Mol Biol Evol 2000, 16:1391-1399.
    • (2000) Mol Biol Evol , vol.16 , pp. 1391-1399
    • Deschavanne, P.1    Giron, A.2    Vilain, J.3    Fagot, G.4    Fertil, B.5
  • 30
    • 0034887748 scopus 로고    scopus 로고
    • Capturing Whole-Genome Characteristics in Short Sequences Using a Naive Bayesian Classifier
    • 311094 11483581 10.1101/gr.186401
    • Sandberg R Winberg G Branden CI Kaske A Ernberg I Coster J Capturing Whole-Genome Characteristics in Short Sequences Using a Naive Bayesian Classifier Genome Res 2001, 11(8):1404-1409. 311094 11483581 10.1101/ gr.186401
    • (2001) Genome Res , vol.11 , Issue.8 , pp. 1404-1409
    • Sandberg, R.1    Winberg, G.2    Branden, C.I.3    Kaske, A.4    Ernberg, I.5    Coster, J.6
  • 31
    • 84856043672 scopus 로고
    • A Mathematical Theory of Communication
    • 379-423
    • Shannon C A Mathematical Theory of Communication Bell Syst Tech J 1948, 27:379-423. 623-656
    • (1948) Bell Syst Tech J , vol.27 , pp. 623-656
    • Shannon, C.1
  • 32
    • 0036301332 scopus 로고    scopus 로고
    • Secondary structure prediction for aligned RNA sequences
    • 10.1016/S0022-2836(02)00308-X 12079347
    • Hofacker I Fekete M Stadler P Secondary structure prediction for aligned RNA sequences Journal of Molecular Biology 2002, 319:1059-1066. 10.1016/ S0022-2836(02)00308-X 12079347
    • (2002) Journal of Molecular Biology , vol.319 , pp. 1059-1066
    • Hofacker, I.1    Fekete, M.2    Stadler, P.3
  • 33
    • 33845362968 scopus 로고    scopus 로고
    • Meauring covariation in RNA alignments: Physical realism improves information measure
    • 10.1093/bioinformatics/btl514 17038338
    • Lindgreen S Gardner P Krogh A Meauring covariation in RNA alignments: physical realism improves information measure Bioinformatics 2006, 22:2988-2995. 10.1093/bioinformatics/btl514 17038338
    • (2006) Bioinformatics , vol.22 , pp. 2988-2995
    • Lindgreen, S.1    Gardner, P.2    Krogh, A.3
  • 34
    • 0034180314 scopus 로고    scopus 로고
    • Species Independence of Mutual Information in Coding and Noncoding Regions
    • 10.1103/PhysRevE.61.5624
    • Grosse I Herzel H Buldyrev S Stanley H Species Independence of Mutual Information in Coding and Noncoding Regions Phys Rev E 2000, 61(5):5624-5629. 10.1103/PhysRevE.61.5624
    • (2000) Phys Rev E , vol.61 , Issue.5 , pp. 5624-5629
    • Grosse, I.1    Herzel, H.2    Buldyrev, S.3    Stanley, H.4
  • 36
    • 33745456505 scopus 로고    scopus 로고
    • Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks
    • Slonim N Elemento O Tavazole S Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks Molecular Systems Biology 2006:2.
    • (2006) Molecular Systems Biology , pp. 2
    • Slonim, N.1    Elemento, O.2    Tavazole, S.3
  • 37
    • 12144284248 scopus 로고    scopus 로고
    • Mutual Information for Examining Correlations in DNA
    • 10.1142/S0219477504001574
    • Berryman M Allison A Abbott D Mutual Information for Examining Correlations in DNA Fluctuation and Noise Letters 2004, 4(2):L237-L246. 10.1142/S0219477504001574
    • (2004) Fluctuation and Noise Letters , vol.4 , Issue.2
    • Berryman, M.1    Allison, A.2    Abbott, D.3
  • 38
    • 42749101835 scopus 로고    scopus 로고
    • Repeats and Correlations in Human DNA Sequences
    • 10.1103/PhysRevE.67.061913
    • Holste D Beirer S Schieg P Grosse I Herzel H Repeats and Correlations in Human DNA Sequences Phys Rev E 2003, 67:061913 1-061913 7. 10.1103/ PhysRevE.67.061913
    • (2003) Phys Rev E , vol.67
    • Holste, D.1    Beirer, S.2    Schieg, P.3    Grosse, I.4    Herzel, H.5
  • 39
    • 13444266307 scopus 로고    scopus 로고
    • Information theory reveals large scale synchronisation of statistical correlations in eukaryote genomes
    • 10.1016/j.gene.2004.11.026 15716116
    • Dehnert M Helm W Hutt MT Information theory reveals large scale synchronisation of statistical correlations in eukaryote genomes Gene 2005, 345:81-90. 10.1016/j.gene.2004.11.026 15716116
    • (2005) Gene , vol.345 , pp. 81-90
    • Dehnert, M.1    Helm, W.2    Hutt, M.T.3
  • 40
    • 33747371129 scopus 로고    scopus 로고
    • Informational structure of two closely related eukaryote genomes
    • 10.1103/PhysRevE.74.021913
    • Dehnert M Helm W Hutt MT Informational structure of two closely related eukaryote genomes Physical Review E 2006, 74:021913-1-021913-9. 10.1103/ PhysRevE.74.021913
    • (2006) Physical Review E , vol.74
    • Dehnert, M.1    Helm, W.2    Hutt, M.T.3
  • 41
    • 25444465885 scopus 로고    scopus 로고
    • Species-specific analysis ofprotein sequences using mutual information
    • 545951 15644130
    • Hummel J Keshvari N weckwerth W Selbig J Species-specific analysis ofprotein sequences using mutual information BMC Bioinformatics 2005:6. 545951 15644130
    • (2005) BMC Bioinformatics , pp. 6
    • Hummel, J.1    Keshvari, N.2    Weckwerth, W.3    Selbig, J.4
  • 42
    • 27944458910 scopus 로고    scopus 로고
    • Using Information Theory to Search for Co-evolving Residues in Proteins
    • 10.1093/bioinformatics/bti671 16159918
    • Martin L Gloor G Dunn S Wahl L Using Information Theory to Search for Co-evolving Residues in Proteins Bioinformatics 2005, 21:4116-4124. 10.1093/bioinformatics/bti671 16159918
    • (2005) Bioinformatics , vol.21 , pp. 4116-4124
    • Martin, L.1    Gloor, G.2    Dunn, S.3    Wahl, L.4


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