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Volumn , Issue , 2010, Pages

Synonymous codon usage bias in the UL47 gene of duck enteritis virus

Author keywords

DEV; Synonymous codon usage bias; UL47

Indexed keywords

C CONTENTS; CODON USAGE; CODON USAGE BIAS; COMPARATIVE ANALYSIS; DEV; EUKARYOTIC EXPRESSION; EXPRESSION SYSTEM; GENETIC HETEROGENEITIES; TARGET GENES; UL47;

EID: 77956134416     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ICBBE.2010.5515888     Document Type: Conference Paper
Times cited : (2)

References (42)
  • 1
    • 0020491327 scopus 로고
    • Codon usage in bacteria: Correlation with gene expressivity
    • Oxford University Press, London, November
    • Gouy. M, Gautier. C, "Codon usage in bacteria: correlation with gene expressivity," Nucleic Acids Res, Oxford University Press, London, vol.10, pp. 7055-7074, November 1982.
    • (1982) Nucleic Acids Res , vol.10 , pp. 7055-7074
    • Gouy, M.1    Gautier, C.2
  • 2
    • 0036786891 scopus 로고    scopus 로고
    • Correlations between Shine-Dalgamo sequences and gene features such as predicted expression levels and operon structures
    • October
    • Ma. J, Campbell. A, Karlin. S, "Correlations between Shine-Dalgamo sequences and gene features such as predicted expression levels and operon structures," J Bacteriol, American Society for Microbiology, United States, vol.184, pp.5733-5745, October 2002.
    • (2002) J Bacteriol, American Society for Microbiology, United States , vol.184 , pp. 5733-5745
    • Ma, J.1    Campbell, A.2    Karlin, S.3
  • 3
    • 0023202933 scopus 로고
    • Codon distribution in vertebrate genes may be used to predict gene length
    • Academic Press, London, October
    • Bains. W, "Codon distribution in vertebrate genes may be used to predict gene length," J.Mol.Biol, Academic Press, London, vol.197, pp:379-388, October 1987.
    • (1987) J.Mol.Biol , vol.197 , pp. 379-388
    • Bains, W.1
  • 4
    • 0037201997 scopus 로고    scopus 로고
    • The base composition of the genes is correlated with the secondary structures of the encoded proteins
    • Amsterdam, 300, October
    • D'Onofrio. G, Ghosh.TC, Bernardi G, "The base composition of the genes is correlated with the secondary structures of the encoded proteins," Gene, Elsevier Science B.V, Amsterdam, vol.300, pp: 179-187, October 2002.
    • (2002) Gene, Elsevier Science B.V , pp. 179-187
    • D'Onofrio, G.1    Ghosh, T.C.2    Bernardi, G.3
  • 5
    • 0019824131 scopus 로고
    • Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system
    • Academic Press, London, September
    • Ikemura. T, "Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system," J.Mol.Biol, Academic Press, London, vol.151, pp:389-409, September 1981.
    • (1981) J.Mol.Biol , vol.151 , pp. 389-409
    • Ikemura, T.1
  • 6
    • 13444269018 scopus 로고    scopus 로고
    • Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes
    • London , Jun
    • Wan. XF, Xu. D, Kleinhofs. A, Zhou. J, "Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes," BMC. Evol. Biol, BioMed Central, London ,vol.4, pp:19, Jun 2004.
    • (2004) BMC. Evol. Biol, BioMed Central , vol.4 , pp. 19
    • Wan, X.F.1    Xu, D.2    Kleinhofs, A.3    Zhou, J.4
  • 7
    • 0030861159 scopus 로고    scopus 로고
    • Evolution of codon usage bias in Drosophila
    • The National Academy of Sciences of the USA, The National Academy of Sciences Beckman Center, July
    • Powell. J. R, Moriyama. E. N, "Evolution of codon usage bias in Drosophila," Proc. Natl. Acad. Sci. U.S.A. The National Academy of Sciences of the USA, The National Academy of Sciences Beckman Center, vol.94, pp:7784-7790, July 1997.
    • (1997) Proc. Natl. Acad. Sci. U.S.A. , vol.94 , pp. 7784-7790
    • Powell, J.R.1    Moriyama, E.N.2
  • 8
    • 0842307105 scopus 로고    scopus 로고
    • The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens
    • Elsevier Science Ireland, Amsterdam, February
    • Gu. W, Zhou. T, Ma. J, Sun. X, Lu. Z, "The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens,"Bio Systems, Elsevier Science Ireland, Amsterdam, vol.73, pp:89-97, February 2004.
    • (2004) Bio Systems , vol.73 , pp. 89-97
    • Gu, W.1    Zhou, T.2    Ma, J.3    Sun, X.4    Lu, Z.5
  • 9
    • 0030569016 scopus 로고    scopus 로고
    • What drives codon choices in human genes
    • Academic Press, London, October
    • Karlin. S, Mrazek. J, "What drives codon choices in human genes," J Mol Biol, Academic Press, London, vol.262, pp:459-472, October 1996.
    • (1996) J Mol Biol , vol.262 , pp. 459-472
    • Karlin, S.1    Mrazek, J.2
  • 10
    • 0028088517 scopus 로고
    • Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes
    • Oxford University Press, London, August
    • Lobry. J. R, Gautier. C, "Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes," Nucleic Acids Res, Oxford University Press, London, vol.22,pp:3174-3180,August 1994.
    • (1994) Nucleic Acids Res , vol.22 , pp. 3174-3180
    • Lobry, J.R.1    Gautier, C.2
  • 11
    • 34548709778 scopus 로고    scopus 로고
    • Synonymous codon usage in different protein secondary structural classes of human genes: Implication for increased non-randomness of GC3 rich genes towards protein stability
    • Springer, Berlin,32, August
    • Mukhopadhyay. P, Basak. S, Ghosh. T. C, "Synonymous codon usage in different protein secondary structural classes of human genes: implication for increased non-randomness of GC3 rich genes towards protein stability," J Biosci, Springer, Berlin,vol.32, pp:947-963, August 2007.
    • (2007) J Biosci , pp. 947-963
    • Mukhopadhyay, P.1    Basak, S.2    Ghosh, T.C.3
  • 12
    • 0035036803 scopus 로고    scopus 로고
    • Evolution of base composition and codon usage bias in the genus Flavivirus
    • Springer-Verlag, Berlin, April
    • Jenkins. G. M, Pagel. M, Gould. E. A, A. Zanotto P. M, Holmes. E. C, "Evolution of base composition and codon usage bias in the genus Flavivirus," J. Mol. Evol, Springer-Verlag, Berlin, vol.52, pp:383-390, April 2001.
    • (2001) J. Mol. Evol , vol.52 , pp. 383-390
    • Jenkins, G.M.1    Pagel, M.2    Gould, E.A.3    Zanotto P M, A.4    Holmes, E.C.5
  • 13
    • 0037372775 scopus 로고    scopus 로고
    • The extent of codon usage bias in human RNA viruses and its evolutionary origin
    • Elsevier Science, Amsterdam, March
    • FJenkins. G. M, Holmes. E. C, "The extent of codon usage bias in human RNA viruses and its evolutionary origin," Virus Res, Elsevier Science, Amsterdam,vol.92, pp:1-7, March 2003.
    • (2003) Virus Res , vol.92 , pp. 1-7
    • Fjenkins, G.M.1    Holmes, E.C.2
  • 14
    • 26244447103 scopus 로고    scopus 로고
    • Relationships among stop codon usage bias, its context, isochores, and gene expression level in various eukaryotes
    • Springer-Verlag , Berlin, October
    • Sun. J, Chen. M, Xu. J, Luo. J, "Relationships among stop codon usage bias, its context, isochores, and gene expression level in various eukaryotes," J. Mol. Evol, Springer-Verlag , Berlin, vol.61, pp:437-444,October 2005.
    • (2005) J. Mol. Evol , vol.61 , pp. 437-444
    • Sun, J.1    Chen, M.2    Xu, J.3    Luo, J.4
  • 15
    • 0020491327 scopus 로고
    • Codon usage in bacteria: Correlation with gene expressivity
    • Oxford University Press, London , November
    • HGouy. M, Gautier. C, "Codon usage in bacteria: correlation with gene expressivity," Nucleic Acids Res, Oxford University Press, London ,vol.10, pp:7055-7074, November 1982.
    • (1982) Nucleic Acids Res , vol.10 , pp. 7055-7074
    • Hgouy, M.1    Gautier, C.2
  • 16
    • 0020363515 scopus 로고
    • Preferential codon usage in prokaryotic genes: The optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes
    • Elsevier/North-Holland, Amsterdam, Jun
    • Grosjean. H, Fiers. W, "Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes," Gene, Elsevier/North-Holland, Amsterdam, vol.18, pp:199-209, Jun 1982.
    • (1982) Gene , vol.18 , pp. 199-209
    • Grosjean, H.1    Fiers, W.2
  • 17
    • 77953930399 scopus 로고    scopus 로고
    • Unusual codon usage bias in low expression genes of Vibrio cholerae
    • Biomedical Informatics Publishing Group, December
    • Basak. S, Mukherjee. I, Choudhury. M, Das. S, "Unusual codon usage bias in low expression genes of Vibrio cholerae," Bioinformation, Biomedical Informatics Publishing Group, vol.3, pp:213-217, December 2008
    • (2008) Bioinformation , vol.3 , pp. 213-217
    • Basak, S.1    Mukherjee, I.2    Choudhury, M.3    Das, S.4
  • 18
    • 63349093676 scopus 로고    scopus 로고
    • Codon usage bias is correlated with gene expression levels in the fission yeast Schizosaccharomyces pombe
    • Molecular Biology Society of Japan/Black well ,14, April
    • THiraokaY, Kawamata. K, Haraguchi. T, Chikashige. Y, "Codon usage bias is correlated with gene expression levels in the fission yeast Schizosaccharomyces pombe," Genes Cells, Molecular Biology Society of Japan/Black well ,vol.14, pp:499-509, April 2009.
    • (2009) Genes Cells , pp. 499-509
    • Thiraoka, Y.1    Kawamata, K.2    Haraguchi, T.3    Chikashige, Y.4
  • 19
    • 67549142080 scopus 로고    scopus 로고
    • Analyzing gene expression from relative codon usage bias in Yeast genome: A statistical significance and biological relevance
    • Elsevier/North-Holland, Amsterdam , August
    • Das. S, Roymondal. U, Sahoo. S, "Analyzing gene expression from relative codon usage bias in Yeast genome: a statistical significance and biological relevance,"Gene,Elsevier/North-Holland, Amsterdam ,vol.443, pp:121-131, August 2009.
    • (2009) Gene , vol.443 , pp. 121-131
    • Das, S.1    Roymondal, U.2    Sahoo, S.3
  • 20
    • 43749119001 scopus 로고    scopus 로고
    • Delving deeper into the unexpected correlation between gene expressivity and codon usage bias of Escherichia coli genome
    • USA , Jun
    • HKahali. B, Basak. S, Ghosh. T. C, "Delving deeper into the unexpected correlation between gene expressivity and codon usage bias of Escherichia coli genome,"Journal of biomolecular structure and dynamics, USA ,vol.25, pp:655-661, Jun 2008.
    • (2008) Journal of Biomolecular Structure and Dynamics , vol.25 , pp. 655-661
    • Hkahali, B.1    Basak, S.2    Ghosh, T.C.3
  • 21
    • 65249112754 scopus 로고    scopus 로고
    • Predicting gene expression level from relative codon usage bias: An application to Escherichia coli genome
    • Oxford University Press, London, February
    • HRoymondal. U, Das. S, Sahoo. S, "Predicting gene expression level from relative codon usage bias: an application to Escherichia coli genome," DNA Res, Oxford University Press, London, vol.16, pp:13-30, February 2009.
    • (2009) DNA Res , vol.16 , pp. 13-30
    • Hroymondal, U.1    Das, S.2    Sahoo, S.3
  • 22
    • 35548932951 scopus 로고    scopus 로고
    • Mutation pressure shapes codon usage in the GC-Rich genome of foot-and-mouth disease virus
    • Springer, Berlin, December
    • Zhong. J, Li.Y, Zhao. S, Liu. S, Zhang. Z, "Mutation pressure shapes codon usage in the GC-Rich genome of foot-and-mouth disease virus," Virus Genes, Springer, Berlin, vol.35, pp:767-776, December 2007.
    • (2007) Virus Genes , vol.35 , pp. 767-776
    • Zhong, J.1    Li, Y.2    Zhao, S.3    Liu, S.4    Zhang, Z.5
  • 23
    • 58149470634 scopus 로고    scopus 로고
    • Analysis of synonymous codon usage in classical swine fever virus
    • Springer, Berlin, 38, February
    • Tao. P.Dai. L,Luo. M,Tang. F,Tien. P, Pan. Z, "Analysis of synonymous codon usage in classical swine fever virus," Virus Genes, Springer, Berlin, vol.38, pp:104-112, February 2009.
    • (2009) Virus Genes , pp. 104-112
    • Tao, P.1    Dai, L.2    Luo, M.3    Tang, F.4    Tien, P.5    Pan, Z.6
  • 24
    • 20844432028 scopus 로고    scopus 로고
    • Bias of base composition and codon usage in Pseudorabies virus genes
    • Elsevier and Science Press, Beijing, Jun
    • Ma. X. R, Xiao. S. B, Fang. L. R, Chen. H. C, "Bias of base composition and codon usage in Pseudorabies virus genes," Acta genetica Sinica, Elsevier and Science Press, Beijing, vol.32, pp:616-624, Jun 2005.
    • (2005) Acta Genetica Sinica , vol.32 , pp. 616-624
    • Ma, X.R.1    Xiao, S.B.2    Fang, L.R.3    Chen, H.C.4
  • 25
    • 0033828846 scopus 로고    scopus 로고
    • Codon usage in nucleopolyhedroviruses
    • Society For General Microbiology, Lodon,81, September
    • Levin. D. B, Whittome. B, "Codon usage in nucleopolyhedroviruses, " J Gen Virol, Society For General Microbiology, Lodon,vol.81, pp:2313-2325, September 2000.
    • (2000) J Gen Virol , pp. 2313-2325
    • Levin, D.B.1    Whittome, B.2
  • 26
    • 19444362139 scopus 로고    scopus 로고
    • Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses
    • Elsevier Science Ireland, Amsterdam, July
    • Zhou. T, Gu. W, Ma. J, Sun. X, Lu. Z, "Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses," Bio Systems, Elsevier Science Ireland, Amsterdam, vol.81, pp:77-86, July 2005.
    • (2005) Bio Systems , vol.81 , pp. 77-86
    • Zhou, T.1    Gu, W.2    Ma, J.3    Sun, X.4    Lu, Z.5
  • 28
    • 30344479949 scopus 로고    scopus 로고
    • Nucleocytoplasmic shuttling of bovine herpesvirus 1 UL47 protein in infected cells
    • American Society For Microbiology, Baltimore, January
    • Verhagen. J, Hutchinson. I, Elliott. G, "Nucleocytoplasmic shuttling of bovine herpesvirus 1 UL47 protein in infected cells ," J Virol, American Society For Microbiology, Baltimore, vol.80, pp:1059-1063, January 2006.
    • (2006) J Virol , vol.80 , pp. 1059-1063
    • Verhagen, J.1    Hutchinson, I.2    Elliott, G.3
  • 29
    • 0035120335 scopus 로고    scopus 로고
    • Nuclear localization and shuttling of herpes simplex virus tegument protein VP13/14
    • American Society For Microbiology, Baltimore, March
    • Donnelly. M, Elliott. G, "Nuclear localization and shuttling of herpes simplex virus tegument protein VP13/14," J Virol, American Society For Microbiology, Baltimore, vol.75, pp:2566-2574, March 2001.
    • (2001) J Virol , vol.75 , pp. 2566-2574
    • Donnelly, M.1    Elliott, G.2
  • 30
    • 0025318864 scopus 로고
    • The 'effective number of codons' used in a gene
    • Elsevier/North-Holland, Amsterdam, March
    • Wright. F, "The 'effective number of codons' used in a gene," Gene, Elsevier/North-Holland, Amsterdam, vol.87, pp:23-29, March 1990.
    • (1990) Gene , vol.87 , pp. 23-29
    • Wright, F.1
  • 31
    • 0031694427 scopus 로고    scopus 로고
    • An evaluation of measures of synonymous codon usage bias
    • Academic Press, London, September
    • Comeron. J.M. Aguade. M, "An evaluation of measures of synonymous codon usage bias," J. Mol. Evol, Academic Press, London, vol.47, pp:268-274, September 1998.
    • (1998) J. Mol. Evol , vol.47 , pp. 268-274
    • Comeron, J.M.1    Aguade, M.2
  • 32
    • 0036667702 scopus 로고    scopus 로고
    • Accounting for background nucleotide composition when measuring codon usage bias
    • Oxford University Press, New York ,19, August
    • Novembre. J. A, "Accounting for background nucleotide composition when measuring codon usage bias," Mol Biol Evol, Oxford University Press, New York ,vol.19, pp:1390-1394, August 2002.
    • (2002) Mol Biol Evol , pp. 1390-1394
    • Novembre, J.A.1
  • 34
    • 0022856787 scopus 로고
    • An evolutionary perspective on synonymous codon usage in unicellular organisms
    • Academic Press, London, February
    • Sharp.P.M, Li.W.H, "An evolutionary perspective on synonymous codon usage in unicellular organisms," J. Mol.Evol, Academic Press, London, vol.24, pp:28-38, February 1986.
    • (1986) J. Mol.Evol , vol.24 , pp. 28-38
    • Sharp, P.M.1    Li, W.H.2
  • 35
    • 0035802429 scopus 로고    scopus 로고
    • Correlation between sequence conservation of the 5′ untranslated region and codon usage bias in Mus musculus genes
    • Elsevier/North-Holland, Amsterdam, October
    • Saikai.H, Washio. T, Saito. R, Shinagawa. A, Itoh. M, Shibata. K, et al, "Correlation between sequence conservation of the 5′ untranslated region and codon usage bias in Mus musculus genes," Gene, Elsevier/North-Holland, Amsterdam, vol.276, pp:101-105, October 2001.
    • (2001) Gene , vol.276 , pp. 101-105
    • Saikai, H.1    Washio, T.2    Saito, R.3    Shinagawa, A.4    Itoh, M.5    Shibata, K.6
  • 36
    • 1642412614 scopus 로고    scopus 로고
    • Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales
    • Elsevier Science, Amsterdam, May
    • Gu. W, Zhou. T, Ma. J, Sun. X, Lu. Z, "Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales," Virus Research, Elsevier Science, Amsterdam, vol.101, pp:155-161, May 2004.
    • (2004) Virus Research , vol.101 , pp. 155-161
    • Gu, W.1    Zhou, T.2    Ma, J.3    Sun, X.4    Lu, Z.5
  • 37
    • 34247847882 scopus 로고    scopus 로고
    • Analysis of synonymous codon usage in Aeropyrum pernix K1 and other Crenarchaeota microorganisms
    • Elsevier, Amsterdam, March
    • Jiang. P, Sun. X, Lu. Z, "Analysis of synonymous codon usage in Aeropyrum pernix K1 and other Crenarchaeota microorganisms," Journal of Genetics and Genomics, Elsevier, Amsterdam, vol.34, pp:275-284, March 2007.
    • (2007) Journal of Genetics and Genomics , vol.34 , pp. 275-284
    • Jiang, P.1    Sun, X.2    Lu, Z.3
  • 38
    • 33344463093 scopus 로고    scopus 로고
    • Synonymous codon usage in environmental chlamydia UWE25 reflects an evolutional divergence from pathogenic chlamydiae
    • Elsevier Science, Amsterdam, March
    • Zhou.T, Sun.X, Lu. Z, "Synonymous codon usage in environmental chlamydia UWE25 reflects an evolutional divergence from pathogenic chlamydiae, "Gene, Elsevier Science, Amsterdam, vol. 368, pp:117-125, March 2006.
    • (2006) Gene , vol.368 , pp. 117-125
    • Zhou, T.1    Sun, X.2    Lu, Z.3
  • 39
    • 0023650543 scopus 로고
    • The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications
    • Oxford University Press, Oxford , February
    • Sharp. P. M, Li. W. H, "The codon adaptation index-a measure of directional synonymous codon usage bias , and its potential applications", Nucleic. Acids. Res, Oxford University Press, Oxford , vol. 15, pp:1281-1295, February 1987.
    • (1987) Nucleic. Acids. Res , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.H.2
  • 40
    • 0026691099 scopus 로고
    • Directional mutation pressure, selective constraints, and genetic equilibria
    • Springer-Verlag, Berlin, February
    • Sueoka. N, "Directional mutation pressure, selective constraints, and genetic equilibria," J. Mol. Evol, Springer-Verlag, Berlin, vol.34,pp:95-114, February 1992.
    • (1992) J. Mol. Evol , vol.34 , pp. 95-114
    • Sueoka, N.1
  • 41
    • 0028568008 scopus 로고
    • Heterogeneity of genomes: Measures and values
    • National Academy of Sciences, Washington, December
    • Karlin. S, Ladunga. I, Blaisdell. B. E, "Heterogeneity of genomes: measures and values," Proc. Natl. Acad. Sci. U.S.A, National Academy of Sciences, Washington, vol.91, pp:12837-12841,December 1994.
    • (1994) Proc. Natl. Acad. Sci. U.S.A , vol.91 , pp. 12837-12841
    • Karlin, S.1    Ladunga, I.2    Blaisdell, B.E.3
  • 42
    • 25444468618 scopus 로고    scopus 로고
    • Noise in gene expression: Origins, consequences, and control
    • American Assn. for the Advancement of Science,Washington, September
    • Raser. J. M, O'Shea. E. K, "Noise in gene expression: origins, consequences, and control," Science, American Assn. for the Advancement of Science,Washington, vol. 309, pp:2010-2013, September 2005.
    • (2005) Science , vol.309 , pp. 2010-2013
    • Raser, J.M.1    O'Shea, E.K.2


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