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Volumn 365, Issue 2, 2007, Pages 241-249

Analysis of the phage sequence space: The benefit of structured information

Author keywords

Bacteriophages; Comparative genomics; Phage classification; Prophage detection

Indexed keywords

VIRUS PROTEIN;

EID: 34547652871     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2007.03.047     Document Type: Short Survey
Times cited : (50)

References (56)
  • 1
    • 0028307501 scopus 로고
    • Tail length determination in bacteriophage T4
    • Abuladze N.K., Gingery M., Tsai J., and Eiserling F.A. Tail length determination in bacteriophage T4. Virology 199 2 (1994) 301-310
    • (1994) Virology , vol.199 , Issue.2 , pp. 301-310
    • Abuladze, N.K.1    Gingery, M.2    Tsai, J.3    Eiserling, F.A.4
  • 4
    • 0036353585 scopus 로고    scopus 로고
    • Streptococcus sanguis secretes CD14-binding proteins that stimulate cytokine synthesis: a clue to the pathogenesis of infective (bacterial) endocarditis?
    • Banks J., Poole S., Nair S.P., Lewthwaite J., Tabona P., McNab R., Wilson M., Paul A., and Henderson B. Streptococcus sanguis secretes CD14-binding proteins that stimulate cytokine synthesis: a clue to the pathogenesis of infective (bacterial) endocarditis?. Microb. Pathog. 32 3 (2002) 105-116
    • (2002) Microb. Pathog. , vol.32 , Issue.3 , pp. 105-116
    • Banks, J.1    Poole, S.2    Nair, S.P.3    Lewthwaite, J.4    Tabona, P.5    McNab, R.6    Wilson, M.7    Paul, A.8    Henderson, B.9
  • 8
    • 33749431828 scopus 로고    scopus 로고
    • Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences
    • Bose M., and Barber R.D. Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences. In Silico Biol. 6 3 (2006) 0020
    • (2006) In Silico Biol. , vol.6 , Issue.3 , pp. 0020
    • Bose, M.1    Barber, R.D.2
  • 9
    • 0036843960 scopus 로고    scopus 로고
    • Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved
    • Boyd E.F., and Brussow H. Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved. Trends Microbiol. 10 11 (2002) 521-529
    • (2002) Trends Microbiol. , vol.10 , Issue.11 , pp. 521-529
    • Boyd, E.F.1    Brussow, H.2
  • 10
    • 0037059610 scopus 로고    scopus 로고
    • Phage genomics: small is beautiful
    • Brussow H., and Hendrix R.W. Phage genomics: small is beautiful. Cell 108 1 (2002) 13-16
    • (2002) Cell , vol.108 , Issue.1 , pp. 13-16
    • Brussow, H.1    Hendrix, R.W.2
  • 11
    • 4544321685 scopus 로고    scopus 로고
    • Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion
    • Brussow H., Canchaya C., and Hardt W.D. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol. Mol. Biol. Rev. 68 3 (2004) 560-602
    • (2004) Microbiol. Mol. Biol. Rev. , vol.68 , Issue.3 , pp. 560-602
    • Brussow, H.1    Canchaya, C.2    Hardt, W.D.3
  • 13
    • 0037825641 scopus 로고    scopus 로고
    • Prophages and bacterial genomics: what have we learned so far?
    • Casjens S. Prophages and bacterial genomics: what have we learned so far?. Mol. Microbiol. 49 2 (2003) 277-300
    • (2003) Mol. Microbiol. , vol.49 , Issue.2 , pp. 277-300
    • Casjens, S.1
  • 14
    • 0000332222 scopus 로고
    • Evolution of the dsDNA-tailed bacteriophage genomes
    • Casjens S., Hatfull G., and Hendrix R. Evolution of the dsDNA-tailed bacteriophage genomes. Semin. Virol. 3 (1992) 383-397
    • (1992) Semin. Virol. , vol.3 , pp. 383-397
    • Casjens, S.1    Hatfull, G.2    Hendrix, R.3
  • 16
    • 0036229271 scopus 로고    scopus 로고
    • Sequence analysis of the lactococcal bacteriophage bIL170: insights into structural proteins and HNH endonucleases in dairy phages
    • Crutz-Le Coq A.M., Cesselin B., Commissaire J., and Anba J. Sequence analysis of the lactococcal bacteriophage bIL170: insights into structural proteins and HNH endonucleases in dairy phages. Microbiology 148 Pt. 4 (2002) 985-1001
    • (2002) Microbiology , vol.148 , Issue.PART 4 , pp. 985-1001
    • Crutz-Le Coq, A.M.1    Cesselin, B.2    Commissaire, J.3    Anba, J.4
  • 17
    • 0033178790 scopus 로고    scopus 로고
    • Comparative sequence analysis of the DNA packaging, head, and tail morphogenesis modules in the temperate cos-site Streptococcus thermophilus bacteriophage Sfi21
    • Desiere F., Lucchini S., and Brussow H. Comparative sequence analysis of the DNA packaging, head, and tail morphogenesis modules in the temperate cos-site Streptococcus thermophilus bacteriophage Sfi21. Virology 260 2 (1999) 244-253
    • (1999) Virology , vol.260 , Issue.2 , pp. 244-253
    • Desiere, F.1    Lucchini, S.2    Brussow, H.3
  • 18
    • 0033806414 scopus 로고    scopus 로고
    • Barriers to intron promiscuity in bacteria
    • Edgell D.R., Belfort M., and Shub D.A. Barriers to intron promiscuity in bacteria. J. Bacteriol. 182 19 (2000) 5281-5289
    • (2000) J. Bacteriol. , vol.182 , Issue.19 , pp. 5281-5289
    • Edgell, D.R.1    Belfort, M.2    Shub, D.A.3
  • 20
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • Enright A.J., Van Dongen S., and Ouzounis C.A. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30 7 (2002) 1575-1584
    • (2002) Nucleic Acids Res. , vol.30 , Issue.7 , pp. 1575-1584
    • Enright, A.J.1    Van Dongen, S.2    Ouzounis, C.A.3
  • 22
    • 0033987383 scopus 로고    scopus 로고
    • Widespread distribution of a group I intron and its three deletion derivatives in the lysin gene of Streptococcus thermophilus bacteriophages
    • Foley S., Bruttin A., and Brussow H. Widespread distribution of a group I intron and its three deletion derivatives in the lysin gene of Streptococcus thermophilus bacteriophages. J. Virol. 74 2 (2000) 611-618
    • (2000) J. Virol. , vol.74 , Issue.2 , pp. 611-618
    • Foley, S.1    Bruttin, A.2    Brussow, H.3
  • 23
    • 33845613147 scopus 로고    scopus 로고
    • Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences
    • Fouts D.E. Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res. 34 20 (2006) 5839-5851
    • (2006) Nucleic Acids Res. , vol.34 , Issue.20 , pp. 5839-5851
    • Fouts, D.E.1
  • 24
    • 0033593367 scopus 로고    scopus 로고
    • Association of holliday-structure resolving endonuclease VII with gp20 from the packaging machine of phage T4
    • Golz S., and Kemper B. Association of holliday-structure resolving endonuclease VII with gp20 from the packaging machine of phage T4. J. Mol. Biol. 285 3 (1999) 1131-1144
    • (1999) J. Mol. Biol. , vol.285 , Issue.3 , pp. 1131-1144
    • Golz, S.1    Kemper, B.2
  • 25
    • 0021266061 scopus 로고
    • Involvement of the invertible G segment in bacteriophage mu tail fiber biosynthesis
    • Grundy F.J., and Howe M.M. Involvement of the invertible G segment in bacteriophage mu tail fiber biosynthesis. Virology 134 2 (1984) 296-317
    • (1984) Virology , vol.134 , Issue.2 , pp. 296-317
    • Grundy, F.J.1    Howe, M.M.2
  • 29
    • 0242323595 scopus 로고    scopus 로고
    • Bacteriophage genomics
    • Hendrix R.W. Bacteriophage genomics. Curr. Opin. Microbiol. 6 5 (2003) 506-511
    • (2003) Curr. Opin. Microbiol. , vol.6 , Issue.5 , pp. 506-511
    • Hendrix, R.W.1
  • 30
    • 0033514996 scopus 로고    scopus 로고
    • Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage
    • Hendrix R.W., Smith M.C., Burns R.N., Ford M.E., and Hatfull G.F. Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage. Proc. Natl. Acad. Sci. U. S. A. 96 5 (1999) 2192-2197
    • (1999) Proc. Natl. Acad. Sci. U. S. A. , vol.96 , Issue.5 , pp. 2192-2197
    • Hendrix, R.W.1    Smith, M.C.2    Burns, R.N.3    Ford, M.E.4    Hatfull, G.F.5
  • 32
    • 0034716946 scopus 로고    scopus 로고
    • Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages
    • Juhala R.J., Ford M.E., Duda R.L., Youlton A., Hatfull G.F., and Hendrix R.W. Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages. J. Mol. Biol. 299 1 (2000) 27-51
    • (2000) J. Mol. Biol. , vol.299 , Issue.1 , pp. 27-51
    • Juhala, R.J.1    Ford, M.E.2    Duda, R.L.3    Youlton, A.4    Hatfull, G.F.5    Hendrix, R.W.6
  • 33
    • 0025200398 scopus 로고
    • Mechanism of length determination in bacteriophage lambda tails
    • Katsura I. Mechanism of length determination in bacteriophage lambda tails. Adv. Biophys. 26 (1990) 1-18
    • (1990) Adv. Biophys. , vol.26 , pp. 1-18
    • Katsura, I.1
  • 34
    • 0036719291 scopus 로고    scopus 로고
    • Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches
    • Lawrence J.G., Hatfull G.F., and Hendrix R.W. Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. J. Bacteriol. 184 17 (2002) 4891-4905
    • (2002) J. Bacteriol. , vol.184 , Issue.17 , pp. 4891-4905
    • Lawrence, J.G.1    Hatfull, G.F.2    Hendrix, R.W.3
  • 35
    • 0347126300 scopus 로고    scopus 로고
    • ACLAME: a CLAssification of Mobile genetic Elements
    • (Database issue)
    • Leplae R., Hebrant A., Wodak S.J., and Toussaint A. ACLAME: a CLAssification of Mobile genetic Elements. Nucleic Acids Res. 32 (2004) D45-D49 (Database issue)
    • (2004) Nucleic Acids Res. , vol.32
    • Leplae, R.1    Hebrant, A.2    Wodak, S.J.3    Toussaint, A.4
  • 36
    • 33750055232 scopus 로고    scopus 로고
    • A first global analysis of plasmid encoded proteins in the ACLAME database
    • Leplae R., Lima-Mendez G., and Toussaint A. A first global analysis of plasmid encoded proteins in the ACLAME database. FEMS Microbiol. Rev. 30 6 (2006) 980-994
    • (2006) FEMS Microbiol. Rev. , vol.30 , Issue.6 , pp. 980-994
    • Leplae, R.1    Lima-Mendez, G.2    Toussaint, A.3
  • 37
    • 1842455969 scopus 로고    scopus 로고
    • Population and evolutionary dynamics of phage therapy
    • Levin B.R., and Bull J.J. Population and evolutionary dynamics of phage therapy. Nat. Rev., Microbiol. 2 2 (2004) 166-173
    • (2004) Nat. Rev., Microbiol. , vol.2 , Issue.2 , pp. 166-173
    • Levin, B.R.1    Bull, J.J.2
  • 38
    • 33645094378 scopus 로고    scopus 로고
    • Protein repertoire of double-stranded DNA bacteriophages
    • Liu J., Glazko G., and Mushegian A. Protein repertoire of double-stranded DNA bacteriophages. Virus Res. 117 1 (2006) 68-80
    • (2006) Virus Res. , vol.117 , Issue.1 , pp. 68-80
    • Liu, J.1    Glazko, G.2    Mushegian, A.3
  • 39
    • 6044228193 scopus 로고    scopus 로고
    • Phage taxonomy: we agree to disagree
    • Nelson D. Phage taxonomy: we agree to disagree. J. Bacteriol. 186 21 (2004) 7029-7031
    • (2004) J. Bacteriol. , vol.186 , Issue.21 , pp. 7029-7031
    • Nelson, D.1
  • 40
  • 41
    • 33645539406 scopus 로고    scopus 로고
    • Origin and evolution of overlapping genes in the family Microviridae
    • Pavesi A. Origin and evolution of overlapping genes in the family Microviridae. J. Gen. Virol. 87 Pt. 4 (2006) 1013-1017
    • (2006) J. Gen. Virol. , vol.87 , Issue.PART 4 , pp. 1013-1017
    • Pavesi, A.1
  • 42
    • 0034715545 scopus 로고    scopus 로고
    • Mutational analysis of two structural genes of the temperate lactococcal bacteriophage TP901-1 involved in tail length determination and baseplate assembly
    • Pedersen M., Ostergaard S., Bresciani J., and Vogensen F.K. Mutational analysis of two structural genes of the temperate lactococcal bacteriophage TP901-1 involved in tail length determination and baseplate assembly. Virology 276 2 (2000) 315-328
    • (2000) Virology , vol.276 , Issue.2 , pp. 315-328
    • Pedersen, M.1    Ostergaard, S.2    Bresciani, J.3    Vogensen, F.K.4
  • 44
    • 0036084146 scopus 로고    scopus 로고
    • InBase: the Intein Database
    • Perler F.B. InBase: the Intein Database. Nucleic Acids Res. 30 1 (2002) 383-384
    • (2002) Nucleic Acids Res. , vol.30 , Issue.1 , pp. 383-384
    • Perler, F.B.1
  • 45
    • 0036330981 scopus 로고    scopus 로고
    • The phage proteomic tree: a genome-based taxonomy for phage
    • Rohwer F., and Edwards R. The phage proteomic tree: a genome-based taxonomy for phage. J. Bacteriol. 184 16 (2002) 4529-4535
    • (2002) J. Bacteriol. , vol.184 , Issue.16 , pp. 4529-4535
    • Rohwer, F.1    Edwards, R.2
  • 46
    • 0034570532 scopus 로고    scopus 로고
    • MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products
    • Serres M.H., and Riley M. MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products. Microb. Comp. Genomics 5 4 (2000) 205-222
    • (2000) Microb. Comp. Genomics , vol.5 , Issue.4 , pp. 205-222
    • Serres, M.H.1    Riley, M.2
  • 47
    • 0037228878 scopus 로고    scopus 로고
    • Twenty thousand ORFan microbial protein families for the biologist?
    • Siew N., and Fischer D. Twenty thousand ORFan microbial protein families for the biologist?. Structure (Cambridge) 11 1 (2003) 7-9
    • (2003) Structure (Cambridge) , vol.11 , Issue.1 , pp. 7-9
    • Siew, N.1    Fischer, D.2
  • 49
    • 0027968068 scopus 로고
    • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 22 (1994) 4673-4680
    • (1994) Nucleic Acids Res. , vol.22 , Issue.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 50
    • 0036152835 scopus 로고    scopus 로고
    • Mobile elements as a combination of functional modules
    • Toussaint A., and Merlin C. Mobile elements as a combination of functional modules. Plasmid 47 1 (2002) 26-35
    • (2002) Plasmid , vol.47 , Issue.1 , pp. 26-35
    • Toussaint, A.1    Merlin, C.2
  • 51
    • 20444460783 scopus 로고    scopus 로고
    • Structural characterization and assembly of the distal tail structure of the temperate lactococcal bacteriophage TP901-1
    • Vegge C.S., Brondsted L., Neve H., Mc Grath S., van Sinderen D., and Vogensen F.K. Structural characterization and assembly of the distal tail structure of the temperate lactococcal bacteriophage TP901-1. J. Bacteriol. 187 12 (2005) 4187-4197
    • (2005) J. Bacteriol. , vol.187 , Issue.12 , pp. 4187-4197
    • Vegge, C.S.1    Brondsted, L.2    Neve, H.3    Mc Grath, S.4    van Sinderen, D.5    Vogensen, F.K.6
  • 52
    • 0033768655 scopus 로고    scopus 로고
    • Holins: the protein clocks of bacteriophage infections
    • Wang I.N., Smith D.L., and Young R. Holins: the protein clocks of bacteriophage infections. Annu. Rev. Microbiol. 54 (2000) 799-825
    • (2000) Annu. Rev. Microbiol. , vol.54 , pp. 799-825
    • Wang, I.N.1    Smith, D.L.2    Young, R.3
  • 53
    • 0014686390 scopus 로고
    • Mapping of deletions and substitutions in heteroduplex DNA molecules of bacteriophage lambda by electron microscopy
    • Westmoreland B.C., Szybalski W., and Ris H. Mapping of deletions and substitutions in heteroduplex DNA molecules of bacteriophage lambda by electron microscopy. Science 163 873 (1969) 1343-1348
    • (1969) Science , vol.163 , Issue.873 , pp. 1343-1348
    • Westmoreland, B.C.1    Szybalski, W.2    Ris, H.3
  • 54
    • 0032858844 scopus 로고    scopus 로고
    • Viruses and nutrient cycles in the sea
    • Wilhelm S.W., and Suttle C.A. Viruses and nutrient cycles in the sea. BioScience 49 10 (1999) 781-788
    • (1999) BioScience , vol.49 , Issue.10 , pp. 781-788
    • Wilhelm, S.W.1    Suttle, C.A.2
  • 55
    • 0342601520 scopus 로고    scopus 로고
    • A rare type of overlapping genes in bacteriophage T4: gene 30.3′ is completely embedded within gene 30.3 by one position downstream
    • Zajanckauskaite A., Malys N., and Nivinskas R. A rare type of overlapping genes in bacteriophage T4: gene 30.3′ is completely embedded within gene 30.3 by one position downstream. Gene 194 2 (1997) 157-162
    • (1997) Gene , vol.194 , Issue.2 , pp. 157-162
    • Zajanckauskaite, A.1    Malys, N.2    Nivinskas, R.3
  • 56
    • 0141765883 scopus 로고    scopus 로고
    • Fabrication of novel biomaterials through molecular self-assembly
    • Zhang S. Fabrication of novel biomaterials through molecular self-assembly. Nat. Biotechnol. 21 10 (2003) 1171-1178
    • (2003) Nat. Biotechnol. , vol.21 , Issue.10 , pp. 1171-1178
    • Zhang, S.1


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