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Volumn 23, Issue 22, 2007, Pages 2978-2986

Annotation of selection strengths in viral genomes

Author keywords

[No Author keywords available]

Indexed keywords

GAG PROTEIN; POL PROTEIN;

EID: 36349026818     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm472     Document Type: Article
Times cited : (10)

References (40)
  • 1
    • 0033214628 scopus 로고    scopus 로고
    • Heuristic approach to deriving models for gene finding
    • Besemer,J. and Borodovsky,M. (1999) Heuristic approach to deriving models for gene finding. Nucleic Acids Res., 27, 3911-3920.
    • (1999) Nucleic Acids Res , vol.27 , pp. 3911-3920
    • Besemer, J.1    Borodovsky, M.2
  • 2
    • 0035875343 scopus 로고    scopus 로고
    • GeneMarkS: A self-training method for prediction of gene starts in microbial genomes: Implications for finding sequence motifs in regulatory regions
    • Besemer,J. et al. (2001) GeneMarkS: A self-training method for prediction of gene starts in microbial genomes: Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res., 29 2607-2618.
    • (2001) Nucleic Acids Res , vol.29 , pp. 2607-2618
    • Besemer, J.1
  • 3
    • 23044471144 scopus 로고    scopus 로고
    • Variability and conservation in hepatitis B virus core protein
    • Chain,B.M. and Myers,R. (2005) Variability and conservation in hepatitis B virus core protein. BMC Microbiol., 5.
    • (2005) BMC Microbiol , vol.5
    • Chain, B.M.1    Myers, R.2
  • 4
    • 34249856374 scopus 로고    scopus 로고
    • Comparative annotation of viral genomes with non-conserved gene structure
    • de Groot,S. et al. (2007) Comparative annotation of viral genomes with non-conserved gene structure. Bioinformatics, 23, 1080-1089.
    • (2007) Bioinformatics , vol.23 , pp. 1080-1089
    • de Groot, S.1
  • 5
    • 3843062475 scopus 로고    scopus 로고
    • Mapping sites of positive selection and amino acid diversification in the HIV genome
    • de Oliveira,T. et al. (2004) Mapping sites of positive selection and amino acid diversification in the HIV genome. Genetics, 167 1047-1058.
    • (2004) Genetics , vol.167 , pp. 1047-1058
    • de Oliveira, T.1
  • 6
    • 0032737463 scopus 로고    scopus 로고
    • Genealogical evidence for positive selection in the nef gene of HIV-1
    • de Zanotto,P. et al. (1999) Genealogical evidence for positive selection in the nef gene of HIV-1. Genetics, 153, 1077-1089.
    • (1999) Genetics , vol.153 , pp. 1077-1089
    • de Zanotto, P.1
  • 7
    • 0028332808 scopus 로고
    • New overlapping gene encoded by the cucumber mosaic virus genome
    • Ding,S.W. et al. (1994) New overlapping gene encoded by the cucumber mosaic virus genome. Virology, 198, 593-601.
    • (1994) Virology , vol.198 , pp. 593-601
    • Ding, S.W.1
  • 9
    • 36448970594 scopus 로고    scopus 로고
    • Felsenstein,J, 1989) PHYLIP, Phylogeny inference package Version 3.2, Cladistics, 5, 164-166
    • Felsenstein,J. (1989) PHYLIP - Phylogeny inference package (Version 3.2). Cladistics, 5, 164-166.
  • 10
    • 13844294363 scopus 로고    scopus 로고
    • Detecting overlapping coding sequences with pairwise alignments
    • Firth,A.E. and Brown,C.M. (2005) Detecting overlapping coding sequences with pairwise alignments. Bioinformatics, 21, 282-292.
    • (2005) Bioinformatics , vol.21 , pp. 282-292
    • Firth, A.E.1    Brown, C.M.2
  • 11
    • 33644837055 scopus 로고    scopus 로고
    • Detecting overlapping coding sequences in virus genomes
    • Firth,A.E. and Brown,C.M. (2006) Detecting overlapping coding sequences in virus genomes. BMC Bioinformatics, 7.
    • (2006) BMC Bioinformatics , vol.7
    • Firth, A.E.1    Brown, C.M.2
  • 12
    • 0345490693 scopus 로고    scopus 로고
    • On dynamics of overlapping genes in bacterial genomes
    • Fukuda,Y. et al. (2003) On dynamics of overlapping genes in bacterial genomes. Gene, 323, 181-187.
    • (2003) Gene , vol.323 , pp. 181-187
    • Fukuda, Y.1
  • 13
    • 0036297144 scopus 로고    scopus 로고
    • Sequence analysis of Potato leafroll virus isolates reveals genetic stability, major evolutionary events and differential selection pressure between overlapping reading frame products
    • Guyader,S. and Ducray,D.G. (2002) Sequence analysis of Potato leafroll virus isolates reveals genetic stability, major evolutionary events and differential selection pressure between overlapping reading frame products. J. Gen. Virol., 83, 1799-1807.
    • (2002) J. Gen. Virol , vol.83 , pp. 1799-1807
    • Guyader, S.1    Ducray, D.G.2
  • 14
    • 0028922694 scopus 로고
    • A maximum-likelihood approach to analyzing nonoverlapping and overlapping reading frame
    • Hein,J. and Støvlbæk,J. (1995) A maximum-likelihood approach to analyzing nonoverlapping and overlapping reading frame. J. Mol. Evol. 40, 181-189.
    • (1995) J. Mol. Evol , vol.40 , pp. 181-189
    • Hein, J.1    Støvlbæk, J.2
  • 15
    • 24944520911 scopus 로고    scopus 로고
    • Patterns of nucleotide difference in overlapping and non-overlapping reading frames of papillomavirus genomes
    • Hughes,A.L. and Hughes,M.A.K. (2005) Patterns of nucleotide difference in overlapping and non-overlapping reading frames of papillomavirus genomes. Virus Res., 113, 81-88.
    • (2005) Virus Res , vol.113 , pp. 81-88
    • Hughes, A.L.1    Hughes, M.A.K.2
  • 16
    • 0037358827 scopus 로고    scopus 로고
    • Detecting recombination in 4-taxa DNA sequence alignments with Bayesian Hidden Markov models and Markov chain Monte Carlo
    • Husmeier,D. and McGuire,G. (2003) Detecting recombination in 4-taxa DNA sequence alignments with Bayesian Hidden Markov models and Markov chain Monte Carlo. Mol. Biol. Evol., 20, 315-337.
    • (2003) Mol. Biol. Evol , vol.20 , pp. 315-337
    • Husmeier, D.1    McGuire, G.2
  • 17
    • 8744308029 scopus 로고    scopus 로고
    • Properties of overlapping genes are conserved across microbial genomes
    • Johnson,Z.I. and Chisholm,S. (2006) Properties of overlapping genes are conserved across microbial genomes. Genome Res., 14, 2268-2272.
    • (2006) Genome Res , vol.14 , pp. 2268-2272
    • Johnson, Z.I.1    Chisholm, S.2
  • 18
    • 0034331806 scopus 로고    scopus 로고
    • Koz1ov,N.N. (2000a) Overlapping genes and variability of the genetic code. Dokl. Biol. Sci., 375, 677-680.
    • Koz1ov,N.N. (2000a) Overlapping genes and variability of the genetic code. Dokl. Biol. Sci., 375, 677-680.
  • 19
    • 0034221509 scopus 로고    scopus 로고
    • Analysis of a set of overlapping genes
    • Kozlov,N.N. (2000b) Analysis of a set of overlapping genes. Dokl. Biochem., 373, 119-122.
    • (2000) Dokl. Biochem , vol.373 , pp. 119-122
    • Kozlov, N.N.1
  • 20
    • 12444259766 scopus 로고    scopus 로고
    • Overlapping genes in vertebrate genomes
    • Makalowska,I. et al. (2005) Overlapping genes in vertebrate genomes. Comput. Biol. Chem., 29, 1-12.
    • (2005) Comput. Biol. Chem , vol.29 , pp. 1-12
    • Makalowska, I.1
  • 21
    • 34447312039 scopus 로고    scopus 로고
    • Using HMMs and observed evolution to annotate viral genomes
    • Advance Access published online on April 13
    • McCauley,S. and Hein,J. (2006) Using HMMs and observed evolution to annotate viral genomes. Bioinformatics, Advance Access published online on April 13, 2006.
    • (2006) Bioinformatics
    • McCauley, S.1    Hein, J.2
  • 22
    • 0345099561 scopus 로고    scopus 로고
    • Improving gene annotation of complete viral genomes
    • Mills,R. et al. (2003) Improving gene annotation of complete viral genomes. Nucleic Acids Res., 31, 7041-7055.
    • (2003) Nucleic Acids Res , vol.31 , pp. 7041-7055
    • Mills, R.1
  • 23
    • 21444455535 scopus 로고    scopus 로고
    • Dual multiple change-point model leads to more accurate recombination detection
    • Minin,V.N. et al. (2005) Dual multiple change-point model leads to more accurate recombination detection. Bioinformatics, 21, 3034-3042.
    • (2005) Bioinformatics , vol.21 , pp. 3034-3042
    • Minin, V.N.1
  • 24
    • 0031030479 scopus 로고    scopus 로고
    • Constrained evolution with respect to gene overlap of Hepatitis B Virus
    • Mizokami,M. et al. (1997) Constrained evolution with respect to gene overlap of Hepatitis B Virus. J. Mol. Evol., 44 (Suppl. 1), 83-90.
    • (1997) J. Mol. Evol , vol.44 , Issue.SUPPL. 1 , pp. 83-90
    • Mizokami, M.1
  • 25
    • 33750332094 scopus 로고    scopus 로고
    • Molecular evolution of hepatitis B virus over 25 Years
    • Osiowy,C. et al. (2006) Molecular evolution of hepatitis B virus over 25 Years. J. Virol., 80, 10307-10314.
    • (2006) J. Virol , vol.80 , pp. 10307-10314
    • Osiowy, C.1
  • 26
    • 0033921799 scopus 로고    scopus 로고
    • Detection of signature sequences in overlapping genes and prediction of a novel overlapping gene in hepatitis G virus
    • Pavesi,A. (2000) Detection of signature sequences in overlapping genes and prediction of a novel overlapping gene in hepatitis G virus. J. Mol. Evol., 50, 284-295.
    • (2000) J. Mol. Evol , vol.50 , pp. 284-295
    • Pavesi, A.1
  • 27
    • 33645539406 scopus 로고    scopus 로고
    • Origin and evolution of overlapping genes in the family Microviridae
    • Pavesi,A. (2006) Origin and evolution of overlapping genes in the family Microviridae. J. Gen. Virol., 87, 1013-1017.
    • (2006) J. Gen. Virol , vol.87 , pp. 1013-1017
    • Pavesi, A.1
  • 28
    • 0030976687 scopus 로고    scopus 로고
    • On the informational content of overlapping genes in prokaryotic and eukaryotic viruses
    • Pavesi,A. et al. (1997) On the informational content of overlapping genes in prokaryotic and eukaryotic viruses. J. Mol. Evol., 44, 625-631.
    • (1997) J. Mol. Evol , vol.44 , pp. 625-631
    • Pavesi, A.1
  • 29
    • 0035035443 scopus 로고    scopus 로고
    • A dependent-rates model and an MCMC-bascd methodology for the maximum-likehhood analysis of sequences with overlapping reading frames
    • Pedersen,A.M. and Jensen,J.L. (2001) A dependent-rates model and an MCMC-bascd methodology for the maximum-likehhood analysis of sequences with overlapping reading frames. Mol. Biol. Evol., 18, 763-776.
    • (2001) Mol. Biol. Evol , vol.18 , pp. 763-776
    • Pedersen, A.M.1    Jensen, J.L.2
  • 30
    • 0037311782 scopus 로고    scopus 로고
    • Gene finding with a hidden Markov model of genome structure and evolution
    • Pedersen,J.S. and Hein,J. (2003) Gene finding with a hidden Markov model of genome structure and evolution. Bioinformatics, 19, 219-227.
    • (2003) Bioinformatics , vol.19 , pp. 219-227
    • Pedersen, J.S.1    Hein, J.2
  • 31
    • 0036575455 scopus 로고    scopus 로고
    • Purifying and directional selection in overlapping prokaryotic genes
    • Rogozin,I. et al. (2002) Purifying and directional selection in overlapping prokaryotic genes. Trends Genet., 18, 228-232.
    • (2002) Trends Genet , vol.18 , pp. 228-232
    • Rogozin, I.1
  • 32
    • 33749827106 scopus 로고    scopus 로고
    • Robust inference of positive selection from recombining coding sequences
    • Scheffler,K. et al. (2006) Robust inference of positive selection from recombining coding sequences. Bioinformatics, 22, 2493-2499.
    • (2006) Bioinformatics , vol.22 , pp. 2493-2499
    • Scheffler, K.1
  • 33
    • 0029095624 scopus 로고
    • Natural selection on the gag, pol, and env genes of human immunodeficiency virus 1 (HIV-1)
    • Seibert,S. et al. (1995) Natural selection on the gag, pol, and env genes of human immunodeficiency virus 1 (HIV-1). Mol. Biol. Evol., 12, 803-813.
    • (1995) Mol. Biol. Evol , vol.12 , pp. 803-813
    • Seibert, S.1
  • 34
    • 1542537849 scopus 로고    scopus 로고
    • Combining phylogenetic and hidden Markov models in biosequence analysis
    • Siepel,A. and Haussler,D. (2004) Combining phylogenetic and hidden Markov models in biosequence analysis. J. Comput. Biol., 11, 413-428.
    • (2004) J. Comput. Biol , vol.11 , pp. 413-428
    • Siepel, A.1    Haussler, D.2
  • 35
    • 0025253821 scopus 로고
    • Analysis of sequence diversity in hypervariable regions of the external glycoprotein of human immunodeficiency virus type 1
    • Simmonds,P. et al. (1990) Analysis of sequence diversity in hypervariable regions of the external glycoprotein of human immunodeficiency virus type 1. J. Virol., 64, 5840-5850.
    • (1990) J. Virol , vol.64 , pp. 5840-5850
    • Simmonds, P.1
  • 36
    • 0027273314 scopus 로고
    • A small highly basic protein is encoded in overlapping reading frame within the P gene of vesicular stomatitis virus
    • Spiropoulou,C.F. and Nichol,S.T. (1993) A small highly basic protein is encoded in overlapping reading frame within the P gene of vesicular stomatitis virus. J. Virol., 67, 3103-3110.
    • (1993) J. Virol , vol.67 , pp. 3103-3110
    • Spiropoulou, C.F.1    Nichol, S.T.2
  • 37
    • 0002671410 scopus 로고
    • Some probabilistic and statistical problems in the analysis of DNA sequences
    • Miura,R.M, ed, American Mathematic Society, Providence, pp
    • Tavaré,S. (1986) Some probabilistic and statistical problems in the analysis of DNA sequences. In: Miura,R.M. (ed.), Some Mathematical Questions in Biology DNA Sequence Analysis. American Mathematic Society, Providence, pp. 57-86.
    • (1986) Some Mathematical Questions in Biology DNA Sequence Analysis , pp. 57-86
    • Tavaré, S.1
  • 38
    • 0027968068 scopus 로고
    • CLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson,J.D. et al. (1994) CLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1
  • 39
    • 0036134765 scopus 로고    scopus 로고
    • Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes
    • Yang,Z.H. and Swanson,W.J. (2002) Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Mol. Biol. Evol., 19, 49-57.
    • (2002) Mol. Biol. Evol , vol.19 , pp. 49-57
    • Yang, Z.H.1    Swanson, W.J.2
  • 40
    • 0035050164 scopus 로고    scopus 로고
    • Evidence for a new hepatitis C virus antigen encoded in an overlapping reading frame
    • Walewski,J.L. et al. (2001) Evidence for a new hepatitis C virus antigen encoded in an overlapping reading frame. RNA, 7, 710-721.
    • (2001) RNA , vol.7 , pp. 710-721
    • Walewski, J.L.1


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