메뉴 건너뛰기




Volumn 18, Issue 6, 2011, Pages 435-449

An integrative method for identifying the over-annotated protein-coding genes in microbial genomes

Author keywords

horizontal gene transfer; microbial genome; protein coding gene; re annotation

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; GENETIC CODE; HORIZONTAL GENE TRANSFER; MICROBIAL GENETICS; MICROORGANISM; NONHUMAN; OPEN READING FRAME;

EID: 82255164229     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dsr030     Document Type: Article
Times cited : (17)

References (61)
  • 1
    • 0033119399 scopus 로고    scopus 로고
    • Errors in genome annotation
    • DOI 10.1016/S0168-9525(99)01706-0, PII S0168952599017060
    • Brenner, S.E. 1999, Errors in genome annotation, Trends Genet., 15, 132-3. (Pubitemid 29155430)
    • (1999) Trends in Genetics , vol.15 , Issue.4 , pp. 132-133
    • Brenner, S.E.1
  • 2
    • 0035313211 scopus 로고    scopus 로고
    • Computational methods for gene annotation: The Arabidopsis genome
    • Yangrae, C. and Virginia, W. 2001, Computational methods for gene annotation: the Arabidopsis genome, Curr. Opin. Biotech., 12, 126-30.
    • (2001) Curr. Opin. Biotech. , vol.12 , pp. 126-130
    • Yangrae, C.1    Virginia, W.2
  • 3
    • 0035424711 scopus 로고    scopus 로고
    • On the total number of genes and their length distribution in complete microbial genomes
    • DOI 10.1016/S0168-9525(01)02372-1, PII S0168952501023721
    • Skovgaard, M., Jensen, L.J., Brunak, S., Ussery, D. and Krogh, A. 2001, On the total number of genes and their length distribution in complete microbial genomes, Trends Genet., 17, 425-8. (Pubitemid 32727225)
    • (2001) Trends in Genetics , vol.17 , Issue.8 , pp. 425-428
    • Skovgaard, M.1    Jensen, L.J.2    Brunak, S.3    Ussery, D.4    Krogh, A.5
  • 4
    • 0035424599 scopus 로고    scopus 로고
    • Intrinsic errors in genome annotation
    • DOI 10.1016/S0168-9525(01)02348-4, PII S0168952501023484
    • Devos, D. and Valencia, A. 2001, Intrinsic errors in genome annotation, Trends Genet., 17, 429-31. (Pubitemid 32727226)
    • (2001) Trends in Genetics , vol.17 , Issue.8 , pp. 429-431
    • Devos, D.1    Valencia, A.2
  • 5
    • 11144239489 scopus 로고    scopus 로고
    • Comprehensive analysis of pseudogenes in prokaryotes: Widespread gene decay and failure of putative horizontally transferred genes
    • Liu, Y., Harrison, P.M., Kunin, V. and Gerstein, M. 2004, Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes, Genome Biol., 5, R64.
    • (2004) Genome Biol. , vol.5
    • Liu, Y.1    Harrison, P.M.2    Kunin, V.3    Gerstein, M.4
  • 6
    • 4344568000 scopus 로고    scopus 로고
    • Genome update: Annotation quality in sequenced microbial genomes
    • Ussery, D.W. and Hallin, P.F. 2004, Genome update: annotation quality in sequenced microbial genomes, Microbiol. SGM, 150, 2015-7. (Pubitemid 39117614)
    • (2004) Microbiology , vol.150 , Issue.7 , pp. 2015-2017
    • Ussery, D.W.1    Hallin, P.F.2
  • 7
    • 34250790725 scopus 로고    scopus 로고
    • Estimating the annotation error rate of curated GO database sequence annotations
    • Jones, C.E., Brown, A.L. and Baumann, U. 2007, Estimating the annotation error rate of curated GO database sequence annotations, BMC Bioinformatics, 8, 170.
    • (2007) BMC Bioinformatics , vol.8 , pp. 170
    • Jones, C.E.1    Brown, A.L.2    Baumann, U.3
  • 8
    • 34147162107 scopus 로고    scopus 로고
    • Genome re-annotation: A wiki solution?
    • Salzberg, S.L. 2007, Genome re-annotation: a wiki solution?, Genome Biol., 8, 102.
    • (2007) Genome Biol. , vol.8 , pp. 102
    • Salzberg, S.L.1
  • 9
    • 47949084234 scopus 로고    scopus 로고
    • Large gene overlaps in prokaryotic genomes: Result of functional constraints or mispredictions?
    • Pallejà, A., Harrington, E.D. and Bork, P. 2008, Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?, BMC Genomics, 9, 335.
    • (2008) BMC Genomics , vol.9 , pp. 335
    • Pallejà, A.1    Harrington, E.D.2    Bork, P.3
  • 10
    • 52449084495 scopus 로고    scopus 로고
    • Identification and correction of abnormal, incomplete and mispredicted proteins in public databases
    • Nagy, A., Hegyi, H., Farkas, K., et al. 2008, Identification and correction of abnormal, incomplete and mispredicted proteins in public databases, BMC Bioinformatics, 9, 353.
    • (2008) BMC Bioinformatics , vol.9 , pp. 353
    • Nagy, A.1    Hegyi, H.2    Farkas, K.3
  • 11
    • 67651091927 scopus 로고    scopus 로고
    • Evaluation of three automated genome annotations for Halorhabdus utahensis
    • Bakke, P., Carney, N., DeLoache, W., et al. 2009, Evaluation of three automated genome annotations for Halorhabdus utahensis, PLoS One, 4, e6291.
    • (2009) PLoS One , vol.4
    • Bakke, P.1    Carney, N.2    Deloache, W.3
  • 12
    • 77954611275 scopus 로고    scopus 로고
    • Using comparative genome analysis to identify problems in annotated microbial genomes
    • Poptsova, M.S. and Gogarten, J.P. 2010, Using comparative genome analysis to identify problems in annotated microbial genomes, Microbiol. SGM, 156, 1909-17.
    • (2010) Microbiol. SGM , vol.156 , pp. 1909-1917
    • Poptsova, M.S.1    Gogarten, J.P.2
  • 13
    • 0034662286 scopus 로고    scopus 로고
    • Recognition of protein coding genes in the yeast genome at better than 95% accuracy based on the Z curve
    • Zhang, C.T. and Wang, J. 2000, Recognition of protein coding genes in the yeast genome at better than 95% accuracy based on the Z curve, Nucleic Acids Res., 28, 2804-14. (Pubitemid 30488023)
    • (2000) Nucleic Acids Research , vol.28 , Issue.14 , pp. 2804-2814
    • Zhang, C.-T.1    Wang, J.2
  • 14
    • 0034572821 scopus 로고    scopus 로고
    • Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs)
    • research0009
    • Natale, D.A., Shankavaram, U.T., Galperin, M.Y., Wolf, Y.I., Aravind, L. and Koonin, E.V. 2000, Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs), Genome Biol., 1, research0009.1-19.
    • (2000) Genome Biol , vol.1 , pp. 1-19
    • Natale, D.A.1    Shankavaram, U.T.2    Galperin, M.Y.3    Wolf, Y.I.4    Aravind, L.5    Koonin, E.V.6
  • 15
    • 0034830866 scopus 로고    scopus 로고
    • Identification of protein-coding genes in the genome of vibrio cholerae with more than 98% accuracy using occurrence frequencies of single nucleotides
    • DOI 10.1046/j.1432-1327.2001.02341.x
    • Wang, J. and Zhang, C.T. 2001, Identification of proteincoding genes in the genome of Vibriocholerae with more than 98% accuracy using occurrence frequencies of single nucleotides, Eur. J. Biochem., 268, 4261-8. (Pubitemid 32862887)
    • (2001) European Journal of Biochemistry , vol.268 , Issue.15 , pp. 4261-4268
    • Wang, J.1    Zhang, C.-T.2
  • 16
    • 0036774642 scopus 로고    scopus 로고
    • Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv
    • Camus, J.C., Pryor, M.J., Médigue, C. and Cole, S.T. 2002, Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv, Microbiology, 148, 2967-73. (Pubitemid 35243696)
    • (2002) Microbiology , vol.148 , Issue.10 , pp. 2967-2973
    • Camus, J.-C.1    Pryor, M.J.2    Medigue, C.3    Cole, S.T.4
  • 17
    • 2142859937 scopus 로고    scopus 로고
    • Re-annotation of genome microbial CoDing-Sequences: Finding new genes and inaccurately annotated genes
    • Bocs, S., Danchin, A. and Medigue, C. 2002, Re-annotation of genome microbial CoDing-Sequences: finding new genes and inaccurately annotated genes, BMC Bioinformatics, 3, 5.
    • (2002) BMC Bioinformatics , vol.3 , pp. 5
    • Bocs, S.1    Danchin, A.2    Medigue, C.3
  • 18
    • 0036640957 scopus 로고    scopus 로고
    • Distinguishing the ORFs from the ELFs: Short bacterial genes and the annotation of genomes
    • DOI 10.1016/S0168-9525(02)02668-9, PII S0168952502026689
    • Ochman, H. 2002, Distinguishing the ORFs from the ELFs:short bacterial genes and the annotation of genomes, Trends Genet., 18, 335-7. (Pubitemid 34804438)
    • (2002) Trends in Genetics , vol.18 , Issue.7 , pp. 335-337
    • Ochman, H.1
  • 19
    • 0043025128 scopus 로고    scopus 로고
    • Gene recognition from questionable ORFs in bacterial and archaeal genomes
    • Chen, L.L. and Zhang, C.T. 2003, Gene recognition from questionable ORFs in bacterial and archaeal genomes, J. Biomol. Struct. Dyn., 21, 99-109.
    • (2003) J. Biomol. Struct. Dyn. , vol.21 , pp. 99-109
    • Chen, L.L.1    Zhang, C.T.2
  • 20
    • 0037251892 scopus 로고    scopus 로고
    • NCBI Reference Sequence project: Update and current status
    • DOI 10.1093/nar/gkg111
    • Pruitt, K.D., Tatusova, T. and Maglott, D.R. 2003, NCBI reference sequence project: update and current status, Nucleic Acids Res., 31, 34-7. (Pubitemid 36150328)
    • (2003) Nucleic Acids Research , vol.31 , Issue.1 , pp. 34-37
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 21
    • 21044451133 scopus 로고    scopus 로고
    • Gene recognition based on nucleotide distribution of ORFs in a hyper-thermophilic crenarchaeon, Aeropyrum pernix K1
    • DOI 10.1093/dnares/11.6.361
    • Guo, F.B., Wang, J. and Zhang, C.T. 2004, Gene recognition based on nucleotide distribution of ORFs in a hyper-thermophilic crenarchaeon, Aeropyrum pernix K1, DNA Res., 11, 361-70. (Pubitemid 40873611)
    • (2004) DNA Research , vol.11 , Issue.6 , pp. 361-370
    • Guo, F.-B.1    Wang, J.2    Zhang, C.-T.3
  • 22
    • 18044389358 scopus 로고    scopus 로고
    • Using purine skews to predict genes in AT-rich poxviruses
    • Silva, M.D. and Upton, C. 2005, Using purine skews to predict genes in AT-rich poxviruses, BMC Genomics, 6, 22.
    • (2005) BMC Genomics , vol.6 , pp. 22
    • Silva, M.D.1    Upton, C.2
  • 23
    • 35648931383 scopus 로고    scopus 로고
    • Re-prediction of protein coding genes in the genome of Amsacta moorei entomopoxvirus
    • Guo, F.B. and Yu, X.J. 2007, Re-prediction of protein coding genes in the genome of Amsacta moorei entomopoxvirus, J. Virol. Methods, 146, 389-92.
    • (2007) J. Virol. Methods , vol.146 , pp. 389-392
    • Guo, F.B.1    Yu, X.J.2
  • 24
    • 37349109147 scopus 로고    scopus 로고
    • Reannotation of hypothetical ORFs in plant pathogen Erwinia carotovora subsp. atroseptica SCRI1043
    • DOI 10.1111/j.1742-4658.2007.06190.x
    • Chen, L.L., Ma, B.G. and Gao, N. 2008, Reannotation of hypothetical ORFs in plant pathogen Erwinia carotovora subsp. atroseptica SCRI1043, FEBS J., 275, 198-206. (Pubitemid 350294076)
    • (2008) FEBS Journal , vol.275 , Issue.1 , pp. 198-206
    • Chen, L.-L.1    Ma, B.-G.2    Gao, N.3
  • 25
    • 71549129512 scopus 로고    scopus 로고
    • Genome reannotation of Escherichia coli CFT073 with new insights into virulence
    • Luo, C.W., Hu, G.Q. and Zhu, H.Q. 2009, Genome reannotation of Escherichia coli CFT073 with new insights into virulence, BMC Genomics, 10, 552.
    • (2009) BMC Genomics , vol.10 , pp. 552
    • Luo, C.W.1    Hu, G.Q.2    Zhu, H.Q.3
  • 26
    • 60849118100 scopus 로고    scopus 로고
    • Identify protein coding genes in the genomes of Aeropyrum pernix K1 and Chlorobium tepidum TLS
    • Guo, F.B. and Lin, Y. 2009, Identify protein coding genes in the genomes of Aeropyrum pernix K1 and Chlorobium tepidum TLS, J. Biomol. Struct. Dyn., 26, 413-20.
    • (2009) J. Biomol. Struct. Dyn. , vol.26 , pp. 413-420
    • Guo, F.B.1    Lin, Y.2
  • 29
    • 0036175276 scopus 로고    scopus 로고
    • The past, present and future of genome-wide re-annotation
    • comment2001
    • Ouzounis, C.A. and Karp, P.D. 2002, The past, present and future of genome-wide re-annotation, Genome Biol., 3, comment2001.1-6.
    • (2002) Genome Biol. , vol.3 , pp. 1-6
    • Ouzounis, C.A.1    Karp, P.D.2
  • 30
    • 0842303618 scopus 로고    scopus 로고
    • YACOP: Enhanced gene prediction obtained by a combination of existing methods
    • Tech, M. and Merkl, R. 2003, YACOP: enhanced gene prediction obtained by a combination of existing methods, In Silico Biol., 3, 441-51. (Pubitemid 38180669)
    • (2003) Silico Biology , vol.3 , Issue.4 , pp. 441-451
    • Tech, M.1    Merkl, R.2
  • 31
    • 3543111963 scopus 로고    scopus 로고
    • Development of joint application strategies for two microbial gene finders
    • DOI 10.1093/bioinformatics/bth137
    • McHardy, A.C., Goesmann, A., Pühler, A. and Meyer, F. 2004, Development of joint application strategies for two microbial gene finders, Bioinformatics, 20, 1622-31. (Pubitemid 39023166)
    • (2004) Bioinformatics , vol.20 , Issue.10 , pp. 1622-1631
    • McHardy, A.C.1    Goesmann, A.2    Puhler, A.3    Meyer, F.4
  • 32
    • 0037444091 scopus 로고    scopus 로고
    • ZCURVE: A new system for recognizing protein coding genes in bacterial and archaeal genomes
    • Guo, F.B., Ou, H.Y. and Zhang, C.T. 2003, ZCURVE: a new system for recognizing protein coding genes in bacterial and archaeal genomes, Nucleic Acids Res., 31, 1780-9.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 1780-1789
    • Guo, F.B.1    Ou, H.Y.2    Zhang, C.T.3
  • 33
    • 0020659327 scopus 로고
    • H curves, a novel method of representation of nucleotide series especially suited for long DNA sequences
    • Hamori, E. and Ruskin, J. 1983, H curves, a novel method of representation of nucleotide series especially suited for long DNA sequences, J. Biol. Chem., 258, 1318-27. (Pubitemid 13139379)
    • (1983) Journal of Biological Chemistry , vol.258 , Issue.2 , pp. 1318-1327
    • Hamori, E.1    Ruskin, J.2
  • 34
    • 77955944760 scopus 로고    scopus 로고
    • A novel construction of genome space with biological geometry
    • Yu, C.L., Liang, Q., Yin, C.C., et al. 2010, A novel construction of genome space with biological geometry, DNA Res., 17, 155-68.
    • (2010) DNA Res. , vol.17 , pp. 155-168
    • Yu, C.L.1    Liang, Q.2    Yin, C.C.3
  • 35
    • 70350066201 scopus 로고    scopus 로고
    • TN curve: A novel 3D graphical representation of DNA sequence based on trinucleotides and its applications
    • Yu, J.F., Sun, X. and Wang, J.H. 2009, TN curve: a novel 3D graphical representation of DNA sequence based on trinucleotides and its applications, J. Theor. Biol., 261, 459-68.
    • (2009) J. Theor. Biol. , vol.261 , pp. 459-468
    • Yu, J.F.1    Sun, X.2    Wang, J.H.3
  • 36
    • 77954304949 scopus 로고    scopus 로고
    • Reannotation of protein coding genes based on an improved graphical representation of DNA sequence
    • Yu, J. F. and Sun, X. 2010, Reannotation of protein coding genes based on an improved graphical representation of DNA sequence, J. Comput. Chem., 31, 2126-35.
    • (2010) J. Comput. Chem. , vol.31 , pp. 2126-2135
    • Yu, J.F.1    Sun, X.2
  • 37
    • 0026059039 scopus 로고
    • Analysis of distribution of bases in the coding sequences by a diagrammatic technique
    • Zhang, C.T. and Zhang, R. 1991, Analysis of distribution of bases in the coding sequences by a diagrammatic technique, Nucleic Acids Res., 19, 6313-7. (Pubitemid 21913057)
    • (1991) Nucleic Acids Research , vol.19 , Issue.22 , pp. 6313-6317
    • Zhang, C.-T.1    Zhang, R.2
  • 38
    • 77951135004 scopus 로고    scopus 로고
    • Analysis of similarities/dissimilarities of DNA sequences based on a novel graphical representation
    • Yu, J.F., Wang, J.H. and Sun, X. 2010, Analysis of similarities/ dissimilarities of DNA sequences based on a novel graphical representation, MATCH Commun. Math. Comput. Chem., 63, 493-512.
    • (2010) MATCH Commun. Math. Comput. Chem. , vol.63 , pp. 493-512
    • Yu, J.F.1    Wang, J.H.2    Sun, X.3
  • 39
    • 1842507532 scopus 로고    scopus 로고
    • Comparison of various algorithms for recognizing short coding sequences of human genes
    • DOI 10.1093/bioinformatics/btg467
    • Gao, F. and Zhang, C.T. 2004, Comparison of various algorithms for recognizing short coding sequences of human genes, Bioinformatics, 20, 673-81. (Pubitemid 38443822)
    • (2004) Bioinformatics , vol.20 , Issue.5 , pp. 673-681
    • Gao, F.1    Zhang, C.-T.2
  • 40
    • 0034708361 scopus 로고    scopus 로고
    • Studies on the relationships between the synonymous codon usage and protein secondary structural units
    • DOI 10.1006/bbrc.2000.2351
    • Gupta, S.K., Majumdar, S., Bhattacharya, T.K. and Ghosh, T.C. 2000, Studies on the relationships between the synonymous codon usage and protein secondary structural units, Biochem. Biophys. Res. Commun., 269, 692-6. (Pubitemid 30440363)
    • (2000) Biochemical and Biophysical Research Communications , vol.269 , Issue.3 , pp. 692-696
    • Gupta, S.K.1    Majumdar, S.2    Bhattacharya, T.K.3    Ghosh, T.C.4
  • 41
    • 0034736516 scopus 로고    scopus 로고
    • Second codon positions of genes and the secondary structures of proteins. Relationships and implications for the origin of the genetic code
    • DOI 10.1016/S0378-1119(00)00521-7, PII S0378111900005217
    • Chiusano, M.L., Alvarez-Valin, F., Giulio, M.D., et al. 2000, Second codon positions of genes and the secondary structures of proteins. Relationships and implications for the origin of the genetic code, Gene, 261, 63-9. (Pubitemid 32103524)
    • (2000) Gene , vol.261 , Issue.1 , pp. 63-69
    • Chiusano, M.L.1    Alvarez-Valin, F.2    Di Giulio, M.3    D'Onofrio, G.4    Ammirato, G.5    Colonna, G.6    Bernardi, G.7
  • 42
    • 0027059264 scopus 로고
    • Assessment of protein coding measures
    • Fickett, J.W. and Tung, C.S. 1992, Assessment of protein coding measures, Nucleic Acids Res., 20, 6441-50. (Pubitemid 23052659)
    • (1992) Nucleic Acids Research , vol.20 , Issue.24 , pp. 6441-6450
    • Fickett, J.W.1    Tung, C.-S.2
  • 43
    • 0030585734 scopus 로고    scopus 로고
    • Evaluation of gene structure prediction programs
    • Burset, M. and Guigo, R. 1996, Evaluation of gene structure prediction programs, Genomics, 34, 353-7.
    • (1996) Genomics , vol.34 , pp. 353-7
    • Burset, M.1    Guigo, R.2
  • 44
    • 0034736520 scopus 로고    scopus 로고
    • Chargaff's legacy
    • DOI 10.1016/S0378-1119(00)00472-8, PII S0378111900004728
    • Forsdyke, D.R. and Mortimer, J.R. 2000, Chargaff's legacy, Gene, 261, 127-37. (Pubitemid 32103530)
    • (2000) Gene , vol.261 , Issue.1 , pp. 127-137
    • Forsdyke, D.R.1    Mortimer, J.R.2
  • 46
    • 0033844505 scopus 로고    scopus 로고
    • The evolution of base composition and phylogenetic inference
    • DOI 10.1016/S0169-5347(00)01934-0, PII S0169534700019340
    • Mooers, A.Ø. and Holmes, E.C. 2000, The evolution of base composition and phylogenetic inference, Trends Ecol. Evol., 9, 365-9. (Pubitemid 30646786)
    • (2000) Trends in Ecology and Evolution , vol.15 , Issue.9 , pp. 365-369
    • Mooers, A.O.1    Holmes, E.C.2
  • 48
    • 0023046211 scopus 로고
    • Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons
    • Sharp, P.M. and Li, W.H. 1986, Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons, Nucleic Acids Res., 14, 7737-49.
    • (1986) Nucleic Acids Res. , vol.14 , pp. 7737-7749
    • Sharp, P.M.1    Li, W.H.2
  • 49
    • 0023194889 scopus 로고
    • Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16S rRNA nucleotide sequences
    • DOI 10.1016/0022-2836(87)90241-5
    • Trifonov, E.N. 1987, Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16 S rRNA nucleotide sequences, J. Mol. Biol., 194, 643-52. (Pubitemid 17076925)
    • (1987) Journal of Molecular Biology , vol.194 , Issue.4 , pp. 643-652
    • Trifonov, E.N.1
  • 50
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
    • Pruitt, K.D., Tatusova, T. and Maglott, D.R. 2007, NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins, Nucleic Acids Res., 35, 61-5.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 61-5
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 51
    • 0033956060 scopus 로고    scopus 로고
    • The COG database: A tool for genome-scale analysis of protein functions and evolution
    • Tatusov, R.L., Galperin, M.Y., Natale, D.A. and Koonin, E.V. 2000, The COG database: a tool for genome-scale analysis of protein functions and evolution, Nucleic Acids Res., 28, 33-6. (Pubitemid 30047708)
    • (2000) Nucleic Acids Research , vol.28 , Issue.1 , pp. 33-36
    • Tatusov, R.L.1    Galperin, M.Y.2    Natale, D.A.3    Koonin, E.V.4
  • 52
    • 28944435815 scopus 로고    scopus 로고
    • Large-scale prokaryotic gene prediction and comparison to genome annotation
    • DOI 10.1093/bioinformatics/bti701
    • Nielsen, P. and Krogh, A. 2005, Large-scale prokaryotic gene prediction and comparison to genome annotation, Bioinformatics, 21, 4322-9. (Pubitemid 41782921)
    • (2005) Bioinformatics , vol.21 , Issue.24 , pp. 4322-4329
    • Nielsen, P.1    Krogh, A.2
  • 53
    • 57149085868 scopus 로고    scopus 로고
    • Genomics of bacteria and archaea: The emerging dynamic view of the prokaryotic world
    • Koonin, E.V. and Wolf, Y.I. 2008, Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world, Nucleic Acids Res., 36, 6688-719.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 6688-719
    • Koonin, E.V.1    Wolf, Y.I.2
  • 54
    • 0037250391 scopus 로고    scopus 로고
    • HGT-DB: A database of putative horizontally transferred genes in prokaryotic complete genomes
    • DOI 10.1093/nar/gkg004
    • Garcia-Vallve, S., Guzman, E., Montero, M.A. and Romeu, A. 2003, HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes, Nucleic Acids Res., 31, 187-9. (Pubitemid 36150361)
    • (2003) Nucleic Acids Research , vol.31 , Issue.1 , pp. 187-189
    • Garcia-Vallve, S.1    Guzman, E.2    Montero, M.A.3    Romeu, A.4
  • 55
    • 30344471824 scopus 로고    scopus 로고
    • Do different surrogate methods detect lateral genetic transfer events of different relative ages?
    • DOI 10.1016/j.tim.2005.11.004, PII S0966842X05003094
    • Ragan, M.A., Harlow, T.J. and Beiko, R.G. 2006, Do different surrogate methods detect lateral genetic transfer events of different relative ages?, Trends Microbiol., 14, 4-8. (Pubitemid 43063184)
    • (2006) Trends in Microbiology , vol.14 , Issue.1 , pp. 4-8
    • Ragan, M.A.1    Harlow, T.J.2    Beiko, R.G.3
  • 56
  • 57
    • 38349118808 scopus 로고    scopus 로고
    • Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses
    • Monier, A., Claverie, J. and Ogata, H. 2007, Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses, BMC Genomics, 8, 456.
    • (2007) BMC Genomics , vol.8 , pp. 456
    • Monier, A.1    Claverie, J.2    Ogata, H.3
  • 58
    • 34547905383 scopus 로고    scopus 로고
    • Detecting laterally transferred genes: Use of entropic clustering methods and genome position
    • DOI 10.1093/nar/gkm204
    • Azad, R.K. and Lawrence, J.G. 2007, Detecting laterally transferred genes: use of entropic clustering methods and genome position, Nucleic Acids Res., 35, 4629-39. (Pubitemid 47250336)
    • (2007) Nucleic Acids Research , vol.35 , Issue.14 , pp. 4629-4639
    • Azad, R.K.1    Lawrence, J.G.2
  • 59
    • 0033670249 scopus 로고    scopus 로고
    • Horizontal gene transfer in bacterial and archaeal complete genomes
    • Garcia-Vallve, S., Romeu, A. and Palau, J. 2000, Horizontal gene transfer in bacterial and archaeal complete genomes, Genome Res., 10, 1719-25.
    • (2000) Genome Res. , vol.10 , pp. 1719-1725
    • Garcia-Vallve, S.1    Romeu, A.2    Palau, J.3
  • 61
    • 0032519353 scopus 로고    scopus 로고
    • GeneMark.hmm: New solutions for gene finding
    • DOI 10.1093/nar/26.4.1107
    • Lukashin, A. and Borodovsky, M. 1998, GeneMark.hmm: new solutions for gene finding, Nucleic Acids Res., 26, 1107-15. (Pubitemid 28291669)
    • (1998) Nucleic Acids Research , vol.26 , Issue.4 , pp. 1107-1115
    • Lukashin, A.V.1    Borodovsky, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.