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Volumn 12, Issue 3, 2005, Pages 331-354

Nonrandom clusters of palindromes in herpesvirus genomes

Author keywords

DNA palindromes; Poisson process approximation; Replication origins; Scan statistics; Wasserstein distance

Indexed keywords

DNA;

EID: 17844366585     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2005.12.331     Document Type: Article
Times cited : (25)

References (53)
  • 1
    • 84972496740 scopus 로고
    • Poisson approximation and the Chen-Stein method
    • Arratia, R., Goldstein, L., and Gordon, L. 1990. Poisson approximation and the Chen-Stein method. Statist. Sci. 5, 403-434.
    • (1990) Statist. Sci. , vol.5 , pp. 403-434
    • Arratia, R.1    Goldstein, L.2    Gordon, L.3
  • 2
    • 0029792949 scopus 로고    scopus 로고
    • Poisson process approximation for sequence repeats, and sequencing by hybridization
    • Arratia, R., Martin, D., Reinert, G., and Waterman, M.S. 1996. Poisson process approximation for sequence repeats, and sequencing by hybridization. J. Comp. Biol. 3, 425-463.
    • (1996) J. Comp. Biol. , vol.3 , pp. 425-463
    • Arratia, R.1    Martin, D.2    Reinert, G.3    Waterman, M.S.4
  • 4
    • 0024638610 scopus 로고
    • Functional mapping a DNA sequence of an equine herpesvirus 1 origin of replication
    • Baumann, R.F., Yalamanchili, V.R.R., and O'Callaghan, D.J. 1988. Functional mapping a DNA sequence of an equine herpesvirus 1 origin of replication. J. Virol. 63(3), 1275-1283.
    • (1988) J. Virol. , vol.63 , Issue.3 , pp. 1275-1283
    • Baumann, R.F.1    Yalamanchili, V.R.R.2    O'Callaghan, D.J.3
  • 6
    • 0034829166 scopus 로고    scopus 로고
    • Central retinal vein occlusion due to herpes zoster as the initial presenting sign in a patient with acquired immunodeficiency syndrome (AIDS)
    • Biswas, J., Deka, S., Padmaja, S., Madhavan, H.N., Kumarasamy, N., and Solomon, S. 2001. Central retinal vein occlusion due to herpes zoster as the initial presenting sign in a patient with acquired immunodeficiency syndrome (AIDS). Occl. Immunol. Inflamm. 9(2), 103-109.
    • (2001) Occl. Immunol. Inflamm. , vol.9 , Issue.2 , pp. 103-109
    • Biswas, J.1    Deka, S.2    Padmaja, S.3    Madhavan, H.N.4    Kumarasamy, N.5    Solomon, S.6
  • 7
    • 17844394829 scopus 로고
    • A restriction endonuclease map for Alcelaphine herpesvirus 1 DNA
    • S.J. O'Brien, ed., Cold Spring Harbor Laboratory Press
    • Bridgen, A. 1991. A restriction endonuclease map for Alcelaphine herpesvirus 1 DNA, in S.J. O'Brien, ed., Genetic Maps, 6th ed., Book 1, Viruses, Cold Spring Harbor Laboratory Press.
    • (1991) Genetic Maps, 6th Ed., Book 1, Viruses
    • Bridgen, A.1
  • 8
    • 0039165347 scopus 로고    scopus 로고
    • Removing logarithms from Poisson process error bounds
    • Brown, T.C., Weinberg, G.V., and Xia, A. 2000. Removing logarithms from Poisson process error bounds. Stochastic Process. Appl. 87, 149-165.
    • (2000) Stochastic Process. Appl. , vol.87 , pp. 149-165
    • Brown, T.C.1    Weinberg, G.V.2    Xia, A.3
  • 9
    • 0035562157 scopus 로고    scopus 로고
    • Stein's method and birth-death processes
    • Brown, T.C., and Xia, A. 2001. Stein's method and birth-death processes. Ann. Probab. 29, 1373-1403.
    • (2001) Ann. Probab. , vol.29 , pp. 1373-1403
    • Brown, T.C.1    Xia, A.2
  • 10
    • 0026502711 scopus 로고
    • Over- and under-representation of short oligonucleotides in DNA sequences
    • Burge, C., Campbell, A.M., and Karlin, S. 1992. Over- and under-representation of short oligonucleotides in DNA sequences. Proc. Natl. Acad. Sci. USA. 89, 1358-1362.
    • (1992) Proc. Natl. Acad. Sci. USA. , vol.89 , pp. 1358-1362
    • Burge, C.1    Campbell, A.M.2    Karlin, S.3
  • 11
    • 4544241299 scopus 로고    scopus 로고
    • Stein's method, Palm theory and Poisson process approximation
    • To appear
    • Chen, L.H.Y., and Xia, A. 2004. Stein's method, Palm theory and Poisson process approximation. To appear in Ann. Probab. 32, 2545-2569.
    • (2004) Ann. Probab. , vol.32 , pp. 2545-2569
    • Chen, L.H.Y.1    Xia, A.2
  • 12
  • 13
    • 84990523621 scopus 로고
    • The minimum of higher order gaps
    • Cressie, N. 1977. The minimum of higher order gaps. Austral. J. Stat. 19, 132-143.
    • (1977) Austral. J. Stat. , vol.19 , pp. 132-143
    • Cressie, N.1
  • 14
    • 0033770967 scopus 로고    scopus 로고
    • The genetic approach to the Epstein-Barr virus: From basic virology to gene therapy
    • Delecluse, H.J., and Hammerschmidt, W. 2000. The genetic approach to the Epstein-Barr virus: From basic virology to gene therapy. J. Clin. Pathol. Mol. Pathol. 53(5), 270-279.
    • (2000) J. Clin. Pathol. Mol. Pathol. , vol.53 , Issue.5 , pp. 270-279
    • Delecluse, H.J.1    Hammerschmidt, W.2
  • 15
    • 0001184792 scopus 로고
    • Poisson approximations for r-scan processes
    • Dembo, A., and Karlin, S. 1992. Poisson approximations for r-scan processes. Ann. Appl. Probab. 2(2), 329-357.
    • (1992) Ann. Appl. Probab. , vol.2 , Issue.2 , pp. 329-357
    • Dembo, A.1    Karlin, S.2
  • 17
    • 0041557570 scopus 로고
    • Epstein-Barr virus
    • O'Brien, S.J., ed., Cold Spring Harbor Laboratory Press
    • Farrell, P.J. 1993. Epstein-Barr virus, in O'Brien, S.J., ed., Genetic Maps, 6th ed., Book 1, Viruses, Cold Spring Harbor Laboratory Press.
    • (1993) Genetic Maps, 6th Ed., Book 1, Viruses
    • Farrell, P.J.1
  • 18
    • 17844374483 scopus 로고    scopus 로고
    • Palindromes in random letter generation: Poisson approximations, rates of growth and Erdös-Rényi laws
    • Ghosh, D., and Godbole, A.P. 1996. Palindromes in random letter generation: Poisson approximations, rates of growth and Erdös-Rényi laws. Lecture Notes in Statistics 114, 99-115.
    • (1996) Lecture Notes in Statistics , vol.114 , pp. 99-115
    • Ghosh, D.1    Godbole, A.P.2
  • 19
    • 0007120637 scopus 로고
    • Approximations and bounds for the distribution of the scan statistics
    • Glaz, J. 1989. Approximations and bounds for the distribution of the scan statistics. J. Am. Statist. Assoc. 84(406), 560-566.
    • (1989) J. Am. Statist. Assoc. , vol.84 , Issue.406 , pp. 560-566
    • Glaz, J.1
  • 20
    • 0041805921 scopus 로고
    • Poisson approximations for the distribution and moments of ordered m-spacings
    • Glaz, J., Naus, J., Roos, M., and Wallenstein, S. 1994. Poisson approximations for the distribution and moments of ordered m-spacings. J. Appl. Prob. 31A, 271-281.
    • (1994) J. Appl. Prob. , vol.31 A , pp. 271-281
    • Glaz, J.1    Naus, J.2    Roos, M.3    Wallenstein, S.4
  • 22
    • 0025228048 scopus 로고
    • Identification of the lytic origin of DNA replication in human cytomegalovirus by a novel approach utilizing ganciclovir-induced chain termination
    • Hamzeh, F.M., Lietman, P.S., Gibson, W., and Hayward, G.S. 1990. Identification of the lytic origin of DNA replication in human cytomegalovirus by a novel approach utilizing ganciclovir-induced chain termination. J. Virol. 64, 6184-6195.
    • (1990) J. Virol. , vol.64 , pp. 6184-6195
    • Hamzeh, F.M.1    Lietman, P.S.2    Gibson, W.3    Hayward, G.S.4
  • 26
    • 0028900683 scopus 로고
    • Epstein-Barr virus in epithelial cell tumors: A breast cancer study
    • Labrecque, L.G., Barnes, D.M., Fentiman, I.S., and Griffin, B.E. 1995. Epstein-Barr virus in epithelial cell tumors: A breast cancer study. Cancer Res. 55(1), 39-45.
    • (1995) Cancer Res. , vol.55 , Issue.1 , pp. 39-45
    • Labrecque, L.G.1    Barnes, D.M.2    Fentiman, I.S.3    Griffin, B.E.4
  • 27
    • 0026049278 scopus 로고
    • An efficient algorithm for identifying matches with errors in multiple long molecular sequences
    • Leung, M.Y., Burge, C., Blaisdell, B.E., and Karlin, S. 1991. An efficient algorithm for identifying matches with errors in multiple long molecular sequences. J. Mol. Biol. 221, 1367-1378.
    • (1991) J. Mol. Biol. , vol.221 , pp. 1367-1378
    • Leung, M.Y.1    Burge, C.2    Blaisdell, B.E.3    Karlin, S.4
  • 28
    • 0029795578 scopus 로고    scopus 로고
    • Over- and underrepresentation of short DNA words in herpesvirus genomes
    • Leung, M.Y., Marsh, G.M., and Speed, T.P. 1996. Over- and underrepresentation of short DNA words in herpesvirus genomes. J. Comp. Biol. 3(3), 345-360.
    • (1996) J. Comp. Biol. , vol.3 , Issue.3 , pp. 345-360
    • Leung, M.Y.1    Marsh, G.M.2    Speed, T.P.3
  • 29
    • 6644224678 scopus 로고
    • Scan statistics and DNA sequence analysis: The search for an origin of replication in a virus
    • Leung, M.Y., Schachtel, G.A., and Yu, H.S. 1994. Scan statistics and DNA sequence analysis: The search for an origin of replication in a virus. Nonlinear World 1, 445-471.
    • (1994) Nonlinear World , vol.1 , pp. 445-471
    • Leung, M.Y.1    Schachtel, G.A.2    Yu, H.S.3
  • 30
    • 4544243440 scopus 로고    scopus 로고
    • Applications of the scan statistic in DNA sequence analysis
    • Glaz, J., and Balakrishnan, N., eds., Birkhauser Publishers
    • Leung, M.Y., and Yamashita, T.E. 1999. Applications of the scan statistic in DNA sequence analysis, in Glaz, J., and Balakrishnan, N., eds., Scan Statistics and Applications, 269-286, Birkhauser Publishers.
    • (1999) Scan Statistics and Applications , pp. 269-286
    • Leung, M.Y.1    Yamashita, T.E.2
  • 31
    • 0026741818 scopus 로고
    • Human cytomegalo-virus origin of DNA replication (oriLyt) resides within a highly complex repetitive region
    • Masse, M.J., Karlin, S., Schachtel, G.A., and Mocarski, E.S. 1992. Human cytomegalo-virus origin of DNA replication (oriLyt) resides within a highly complex repetitive region. Proc. Natl. Acad. Sci. USA. 89, 5246-5250.
    • (1992) Proc. Natl. Acad. Sci. USA. , vol.89 , pp. 5246-5250
    • Masse, M.J.1    Karlin, S.2    Schachtel, G.A.3    Mocarski, E.S.4
  • 33
    • 0032584101 scopus 로고    scopus 로고
    • Strand compositional asymmetry in bacterial and large viral genomes
    • Mrazek, J., and Karlin, S. 1998. Strand compositional asymmetry in bacterial and large viral genomes. Proc. Natl. Acad. Sci. USA 95, 3720-3725.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 3720-3725
    • Mrazek, J.1    Karlin, S.2
  • 34
    • 0001701628 scopus 로고
    • The distribution of the size of the maximum cluster of points on a line
    • Naus, J.I. 1965. The distribution of the size of the maximum cluster of points on a line. J. Am. Statist. Assoc. 60, 532-538.
    • (1965) J. Am. Statist. Assoc. , vol.60 , pp. 532-538
    • Naus, J.I.1
  • 35
    • 0036010593 scopus 로고    scopus 로고
    • DNA replication joins the revolution: Whole-genome views of DNA replication in budding yeast
    • Newlon, C.S., and Theis, J.F. 2002. DNA replication joins the revolution: Whole-genome views of DNA replication in budding yeast. BioEssays 24, 300-304.
    • (2002) BioEssays , vol.24 , pp. 300-304
    • Newlon, C.S.1    Theis, J.F.2
  • 36
    • 0023664163 scopus 로고
    • 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
    • Phillips, G., Arnold, J., and Ivarie, R. 1987. 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, 2627-2638.
    • (1987) Nucl. Acids Res. , vol.15 , pp. 2627-2638
    • Phillips, G.1    Arnold, J.2    Ivarie, R.3
  • 37
    • 0000375303 scopus 로고
    • Finding words with unexpected frequencies in DNA sequences
    • Prum, B., Rodolphe, F., and De Turckheim, E. 1995. Finding words with unexpected frequencies in DNA sequences. J. R. Statist. Soc. B 57(1), 205-220.
    • (1995) J. R. Statist. Soc. B , vol.57 , Issue.1 , pp. 205-220
    • Prum, B.1    Rodolphe, F.2    De Turckheim, E.3
  • 38
    • 0031902984 scopus 로고    scopus 로고
    • Compound Poisson and Poisson process approximations for occurrences of multiple words in Markov chains
    • Reinert, G., and Schbath, S. 1998. Compound Poisson and Poisson process approximations for occurrences of multiple words in Markov chains. J. Comp. Biol. 5, 223-253.
    • (1998) J. Comp. Biol. , vol.5 , pp. 223-253
    • Reinert, G.1    Schbath, S.2
  • 39
    • 0034125366 scopus 로고    scopus 로고
    • Probabilistic and statistical properties of words: An overview
    • Reinert, G., Schbath, S., and Waterman, M.S. 2000. Probabilistic and statistical properties of words: An overview. J. Comp. Biol. 7, 1-46.
    • (2000) J. Comp. Biol. , vol.7 , pp. 1-46
    • Reinert, G.1    Schbath, S.2    Waterman, M.S.3
  • 40
    • 0021887852 scopus 로고
    • A putative origin of replication of plasmids derived from Epstein-Barr virus is composed of two cis-acting components
    • Reisman, D., Yates, J., and Sugden, B. 1985. A putative origin of replication of plasmids derived from Epstein-Barr virus is composed of two cis-acting components. Mol. Cell. Biol. 5, 1822-1832.
    • (1985) Mol. Cell. Biol. , vol.5 , pp. 1822-1832
    • Reisman, D.1    Yates, J.2    Sugden, B.3
  • 41
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The European Molecular Biology Open Software Suite
    • Rice, P., Longden, I., and Bleasby, A. 2000. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 16(6), 276-277.
    • (2000) Trends Genet. , vol.16 , Issue.6 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 42
    • 0011568576 scopus 로고
    • Compound Poisson approximations for the numbers of extreme spacings
    • Roos, M. 1993. Compound Poisson approximations for the numbers of extreme spacings. Adv. Appl. Probab. 25, 847-874.
    • (1993) Adv. Appl. Probab. , vol.25 , pp. 847-874
    • Roos, M.1
  • 44
    • 84996141000 scopus 로고
    • Compound Poisson approximation of word counts in DNA sequences
    • Schbath, S. 1995. Compound Poisson approximation of word counts in DNA sequences. ESAIM: Prob. and Stat. 1, 1-16.
    • (1995) ESAIM: Prob. and Stat. , vol.1 , pp. 1-16
    • Schbath, S.1
  • 45
    • 0000457248 scopus 로고
    • A bound for the error in the normal approximation to the distribution of a sum of dependent random variables
    • Stein, C. 1972. A bound for the error in the normal approximation to the distribution of a sum of dependent random variables. Proc. 6th Berkeley Symp. Math Statist. Probab. 2, 583-602.
    • (1972) Proc. 6th Berkeley Symp. Math Statist. Probab. , vol.2 , pp. 583-602
    • Stein, C.1
  • 46
    • 0036165501 scopus 로고    scopus 로고
    • In the beginning: A viral origin exploits the cell
    • Sugden, B. 2002. In the beginning: A viral origin exploits the cell. Trends Biochem. Sci. 27(1), 1-3.
    • (2002) Trends Biochem. Sci. , vol.27 , Issue.1 , pp. 1-3
    • Sugden, B.1
  • 47
    • 0003304127 scopus 로고
    • Some statistical aspects of the primary structure of nucleotide sequences
    • Waterman, M.S., ed., CRC Press, Boca Raton, FL
    • Tavaré, S., and Giddings, W. 1989. Some statistical aspects of the primary structure of nucleotide sequences, in Waterman, M.S., ed., Mathematical Methods for DNA Sequences, CRC Press, Boca Raton, FL.
    • (1989) Mathematical Methods for DNA Sequences
    • Tavaré, S.1    Giddings, W.2
  • 48
    • 0028836961 scopus 로고
    • Concurrent herpes simplex type 1 necrotizing encephalitis, cytomegalovirus ventriculoencephalitis and cerebral lymphoma in an AIDS patient
    • Vital, C., Monlun, E., Vital, A., Martin-Negrier, M.L., Cales, V., Leger, F., Longy-Boursier, M., Le Bras, M., and Bloch, B. 1995. Concurrent herpes simplex type 1 necrotizing encephalitis, cytomegalovirus ventriculoencephalitis and cerebral lymphoma in an AIDS patient. Acta pathologica 89(1), 105-108.
    • (1995) Acta Pathologica , vol.89 , Issue.1 , pp. 105-108
    • Vital, C.1    Monlun, E.2    Vital, A.3    Martin-Negrier, M.L.4    Cales, V.5    Leger, F.6    Longy-Boursier, M.7    Le Bras, M.8    Bloch, B.9
  • 52
    • 0023851387 scopus 로고
    • An enhancer element in the short unique region of human cytomegalo virus regulates the production of a group of abundant immediate early transcripts
    • Weston, K. 1988. An enhancer element in the short unique region of human cytomegalo virus regulates the production of a group of abundant immediate early transcripts. Virology 162, 406-416.
    • (1988) Virology , vol.162 , pp. 406-416
    • Weston, K.1
  • 53
    • 0031949591 scopus 로고    scopus 로고
    • Human cytomegalovirus oriLyt sequence requirements
    • Zhu, Y., Huang, L., and Anders, D.G. 1998. Human cytomegalovirus oriLyt sequence requirements. J. Virol. 72, 4989-4996.
    • (1998) J. Virol. , vol.72 , pp. 4989-4996
    • Zhu, Y.1    Huang, L.2    Anders, D.G.3


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