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In Sffamily Identification of Genes in Bacteriophage DNA

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Bacteriophages

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 502))

Abstract

One of the most satisfying aspects of a genome sequencing project is the identification of the genes contained within it.These are of two types: those which encode tRNAs and those which produce proteins. After a general introduction on the properties of protein-encoding genes and the utility of the Basic Local Alignment Search Tool (BLASTX) to identify genes through homologs, a variety of tools are discussed by their creators. These include for genome annotation: GeneMark, Artemis, and BASys; and, for genome comparisons: Artemis Comparison Tool (ACT), Mauve, CoreGenes, and GeneOrder.

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References

  1. Grigoriev, A. 1999. Strand-specific compositional asymmetries in double-stranded DNA viruses. Virus Research 60:1–19.

    Article  CAS  PubMed  Google Scholar 

  2. Casjens, S., D.A. Winn-Stapley, E.B. Gilcrease, R. Morona, C. Kuhlewein, J.E. Chua, P.A. Manning, and A.J. Clark. 2004. The Chromosome of Shigella flexneri Bacteriophage Sf6: Complete Nucleotide Sequence, Genetic Mosaicism, and DNA Packaging. Journal of Molecular Biology 339:379–394.

    Article  CAS  PubMed  Google Scholar 

  3. Hu, F., K. Zhang, Y. Tan, X. Jin, J. Zhu, J. Huang, X. Rao, X. Shen, and X. Hu. 2003. Complete genome sequence of Pseudomonas aeruginosa bacteriophage PaP3. GenBank Accession Number NC_004466.

    Google Scholar 

  4. Mann, N.H., A. Cook, M. Clockie, and A. Millard. 2005. Sequence analysis of the genome of bacteriophage S-PM2. Cyanophage S-PM2. GenBank Accession Number NC_006820.

    Google Scholar 

  5. Lindell, D., M.B. Sullivan, Z.I. Johnson, A.C. Tolonen, F. Rohwer, and S.W. Crisholm. 2005. Prochlorococcus cyanophage genomes. Cyanophage P-SSM2. GenBank Accession Number NC_006883.

    Google Scholar 

  6. Nolan, J.M., V. Petrov, C. Bertrand, H.M. Krisch, and J.D. Karam. 2005. Comparative analysis of the Aeromonas bacteriophage 31 genome. GenBank Accession Number NC_007022.

    Google Scholar 

  7. Sibbald, M.J. and A.M. Kropinski. 1999. Transfer RNA genes and their significance to codon usage in the Pseudomonas aeruginosa lamboid bacteriophage D3. Canadian Journal of Microbiology 45:791–796.

    Article  PubMed  Google Scholar 

  8. Miller, E.S., J.F. Heidelberg, J.A. Eisen, W.C. Nelson, A.S. Durkin, A. Ciecko, T.V. Feldblyum, O. White, et al. 2003. Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage. Journal of Bacteriology 185:5220–5233.

    Article  CAS  PubMed  Google Scholar 

  9. Miller, E.C., E. Kutter, G. Mosig, F. Arisaka, T. Kunisawa, and W. Rüger. 2003. Bacteriophage T4 genome. Microbiology and Molecular Biology Reviews 67: 86–156.

    Article  CAS  PubMed  Google Scholar 

  10. Dodd, I.B. and J.B. Egan. 2005. Bacteriophage 186 complete genome. Enterobacteria phage 186. GenBank Accession Number NC_001317.

    Google Scholar 

  11. Lobocka, M.B., D.J. Rose, G. Plunkett, III, M. Rusin, A. Samojedny, H. Lehnherr, M.B. Yarmolinsky, and F.R. Blattner. 2004. Genome of bacteriophage P1. Journal of Bacteriology 186:7032–7068.

    Article  CAS  PubMed  Google Scholar 

  12. Ksenzenko, V.N., A.V. Kaliman, A.I. Krutilina, and M.G. Shlyapnikov. 200. Bacteriophage T5 complete genome. Enterobacterial phage T5. GenBank Accession Number NC_005859.

    Google Scholar 

  13. Srirannganathan, N., J.M. Whichard, F.W. Pierson, and V. Kapur. 2005. Bacteriophage Felix O1: Genetic characterization. GenBank Accesion Number NC_005282.

    Google Scholar 

  14. Smith, M.C., R.N. Burns, S.E. Wilson, and M.A. Gregory. 1999. The complete genome sequence of the Streptomyces temperate phage straight \(\phi\)C31: evolutionary relationships to other viruses. Nucleic Acids Research 27:2145–2155.

    Article  CAS  PubMed  Google Scholar 

  15. Gregory, M.A., R. Till, and M.C. Smith. 2003. Integration site for Streptomyces phage \(\phi\)BT1 and development of site-specific integrating vectors. Journal of Bacteriology 185: 5320–5323.

    Article  CAS  PubMed  Google Scholar 

  16. Pedulla, M.L., M.E. Ford, J.M. Houtz, T. Karthikeyan, C. Wadsworth, J.A. Lewis, D.Jacobs-Sera, J. Falbo, et al. 2003. Origins of highly mosaic mycobacteriophage genomes. Cell 113: 171–182.

    Article  CAS  PubMed  Google Scholar 

  17. Ford, M.E., G.J. Sardis, A.E. Belanger, R.W. Hendrix, and G.F. Hatfull. 1998. Genome structure of mycobacteriophage D29: Implications for phage evolution. Journal of Molecular Biology 279:143–164.

    Article  CAS  PubMed  Google Scholar 

  18. Zimmer, M., E. Sattelberger, R.B. Inman, R. Calendar, and M.J. Loessner. 2003. Genome and proteome of Listeria monocytogenes phage PSA: an unusual case for programmed +1 translational frameshifting in structural protein synthesis. Molecular Microbiology 50:303–317.

    Article  CAS  PubMed  Google Scholar 

  19. Lowe, T.M. and S.R. Eddy. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 25:955–964.

    Article  CAS  PubMed  Google Scholar 

  20. Laslett, D., Canback, B. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Research 32(1): 11–16.

    Article  CAS  PubMed  Google Scholar 

  21. Newton, G.J., C. Daniels, L.L. Burrows, A.M. Kropinski, A.J. Clarke, and J.S. Lam. 2001. Three-component-mediated serotype conversion in Pseudomonas aeruginosa by bacteriophage D3. Molecular Microbiology 39:1237–1247.

    Article  CAS  PubMed  Google Scholar 

  22. Lindell, D., M.B. Sullivan, Z. I. Johnson, A.C. Tolonen, F. Rohwer, and S. W. Chisholm. 2004. Transfer of photosynthesis genes to and from Prochlorococcus viruses. Proceedings of the National Academy of Sciences of the United States of America 101:11013–11018.

    Article  CAS  PubMed  Google Scholar 

  23. Villegas, A. and A.M. Kropinski. 2008. AAA An analysis of initiation codon utilization in the domain Bacteria – concerms about the quality of bacterial genome annotation Microbiology 154: 2559–2561.

    CAS  Google Scholar 

  24. Shine, J. and L. Dalgarno. 1975. Terminal-sequence analysis of bacterial ribosomal RNA. Correlation between the \(3^{\prime}\)-terminal-polypyrimidine sequence of 16-S RNA and translational specificity of the ribosome. European Journal of Biochemistry 57:221–230.

    Article  CAS  PubMed  Google Scholar 

  25. Shine, J. and L. Dalgarno. 1974. The \(3^{\prime}\)-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proceedings of the National Academy of Sciences of the United States of America 71:1342–1346.

    Article  CAS  PubMed  Google Scholar 

  26. Farinha, M.A. and A.M. Kropinski. 1997. Overexpression, purification, and analysis of the c1 repressor protein of Pseudomonas aeruginosa bacteriophage D3. Canadian Journal of Microbiology 43:220–226.

    Article  CAS  PubMed  Google Scholar 

  27. Hendrix, R.W. 2002. Bacteriophages: evolution of the majority. Theoretical Population Biology 61:471–480.

    Article  PubMed  Google Scholar 

  28. Hendrix, R.W., M.C. Smith, R.N. Burns, M.E. Ford, and G.F. Hatfull. 1999. Evolutionary relationships among diverse bacteriophages and prophages: all the world’s a phage. Proceedings of the National Academy of Sciences of the United States of America 96:2192–2197.

    Article  CAS  PubMed  Google Scholar 

  29. Chibani-Chennoufi, S., C. Canchaya, A. Bruttin, and H. Brussow. 2004. Comparative genomics of the T4-Like Escherichia coli phage JS98: implications for the evolution of T4 phages. Journal of Bacteriology 186: 8276–8286.

    Article  CAS  PubMed  Google Scholar 

  30. O’Flaherty, S., A. Coffey, R.Edwards, W. Meaney, G.F. Fitzgerald, and R.P. Ross. 2004. Genome of staphylococcal phage K: a new lineage of Myoviridae infecting gram-positive bacteria with a low \(\mathrm{G}+\mathrm{C}\) content. Journal of Bacteriology 186: 2862–2871.

    Article  PubMed  Google Scholar 

  31. Scholl, D. and C. Merril. 2005. The Genome of bacteriophage K1F, a T7-Like phage that has acquired the ability to replicate on K1 strains of Escherichia coli. Journal of Bacteriology 187:8499–8503.

    Article  CAS  PubMed  Google Scholar 

  32. Bonocora, R.P. and D.A. Shub. 2004. A self-splicing group I intron in DNA polymerase genes of T7-like bacteriophages. Journal of Bacteriology 186:8153–8155.

    Article  CAS  PubMed  Google Scholar 

  33. Foley, S., A. Bruttin, and H. Brussow. 2000. Widespread distribution of a group I intron and its three deletion derivatives in the lysin gene of Streptococcus thermophilus bacteriophages. Journal of Virology 74: 611–618.

    Article  CAS  PubMed  Google Scholar 

  34. Nelson, D., R. Schuch, S. Zhu, D.M. T scherne, and V.A. Fischetti. 2003. Genomic sequence of C1, the first streptococcal phage. Journal of Bacteriology 185:3325–3332.

    Article  CAS  PubMed  Google Scholar 

  35. Seegers, J.F., G.S. Mc, M.O’Connell-Motherway, E.K. Arendt, G.M. van de, M. Creaven, G.F. Fitzgerald, and S.D. van. 2004. Molecular and transcriptional analysis of the temperate lactococcal bacteriophage Tuc2009. Virology 329:40–52.

    Article  CAS  PubMed  Google Scholar 

  36. van, S.D., H. Karsens, J. Kok, P. Terpstra, M.H. Ruiters, G. Venema, and A. Nauta. 1996. Sequence analysis and molecular characterization of the temperate lactococcal bacteriophage r1t. Molecular Microbiology 19: 1343–1355.

    Article  Google Scholar 

  37. Landthaler, M. and D.A. Shub. 2003. The nicking homing endonuclease I-BasI is encoded by a group I intron in the DNA polymerase gene of the Bacillus thuringiensis phage Bastille. Nucleic Acids Research 31:3071–3077.

    Article  CAS  PubMed  Google Scholar 

  38. Lazarevic, V., B. Soldo, A. Dusterhoft, H. Hilbert, C. Mauel, and D. Karamata. 1998. Introns and intein coding sequence in the ribonucleotide reductase genes of Bacillus subtilis temperate bacteriophage SPbeta. Proceedings of the National Academy of Sciences of the United States of America 95: 1692–1697.

    Article  CAS  PubMed  Google Scholar 

  39. Mann, N.H., M.R. Clokie, A. Millard, A. Cook, W.H. Wilson, P. J. Wheatley, A. Letarov, and H. M. Krisch. 2005. The genome of S-PM2, a “photosynthetic” T4-type bacteriophage that infects marine Synechococcus strains. Journal of Bacteriology 187: 3188–3200.

    Article  CAS  PubMed  Google Scholar 

  40. Landthaler, M. and D.A. Shub. 1999. Unexpected abundance of self-splicing introns in the genome of bacteriophage Twort: introns in multiple genes, a single gene with three introns, and exon skipping by group I ribozymes. Proceedings of the National Academy of Sciences of the United States of America 96:7005–7010.

    Article  CAS  PubMed  Google Scholar 

  41. Condron, B.G., J.F. Atkins, and R.F. Gesteland. 1991. Framshifting in gene 10 of bacteriophage T7. Journal of Bacteriology 173:6998–7003.

    CAS  PubMed  Google Scholar 

  42. Levin, M.E., R.W. Hendrix, and S.R. Casjens. 1993. A programmed translational frameshift is required for the synthesis of a bacteriophage lambda tail assembly protein. Journal of Molecular Biology 234: 124–139.

    Article  CAS  PubMed  Google Scholar 

  43. Christie, G.E., L.M. Temple, B.A. Bartlett, and T.S. Goodwin. 2002. Programmed translational frameshift in the bacteriophage P2 FETUD tail gene operon. Journal of Bacteriology 184:6522–6531.

    Article  CAS  PubMed  Google Scholar 

  44. Kolla, V., M. Chakravorty, B. Pandey, S.M. Srinivasula, A. Mukherjee, and G. Litwack. 2000. Synthesis of a bacteriophage MB78 late protein by novel ribosomal frameshifting. Gene 254:209–217.

    Article  CAS  PubMed  Google Scholar 

  45. Farabaugh, P.J. 1996. Programmed translational frameshifting. Annual Review of Genetics 30:507–528.

    Article  CAS  PubMed  Google Scholar 

  46. Reeder, J. and R. Giegerich. 2004. Design implementation and evaluation of a practical pseudoknots folding algorithm based upon thermodynamics. BMC Bioinformatics 5: 104–115.

    Article  PubMed  Google Scholar 

  47. Kropinski, A.M., M. Hayward, M.D. Agnew, and K.F. Jarrell. 2005. The genome of BCJA1c: a bacteriophage active against the alkaliphilic bacterium, Bacillus clarkii. Extremophiles 9:99–109.

    Article  CAS  PubMed  Google Scholar 

  48. Altschul, S.F., W. Gish, W. Miller, E.W. Myers, and D.J. Lipman. 1990. Basic local alignment search tool. Journal of Molecular Biology 215:403–410.

    CAS  PubMed  Google Scholar 

  49. Rutherford, K., J. Parkhill, J. Crook, T. Horsnell, P. Rice, M. A. Rajandream, and B.Barrell. 2000. Artemis: sequence visualization and annotation. Bioinformatics 16:944–945.

    Article  CAS  PubMed  Google Scholar 

  50. Besemer, J. and M. Borodovsky. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Research 33:W451–W454.

    Article  CAS  PubMed  Google Scholar 

  51. Borodovsky, M. and J. McIninch. 1993. GeneMark: parallel gene recognition for both DNA strands. Computers & Chemistry 17:123–133.

    Article  CAS  Google Scholar 

  52. Lukashin, A. and M. Borodovsky. 1998. GeneMark.hmm: new solutions for gene finding. Nucleic Acids Research 26:1107–1115.

    Article  CAS  PubMed  Google Scholar 

  53. Besemer, J., A. Lomsadze, M. Borodovsky, J. Besemer, A. Lomsadze, and M. Borodovsky. 2001. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Research 29:2607–2618.

    Article  CAS  PubMed  Google Scholar 

  54. Mills, R., M.Rozanov, A. Lomsadze, T. Tatusova, M. Borodovsky, R. Mills, M. Rozanov, A. Lomsadze, et al. 2003. Improving gene annotation of complete viral genomes. Nucleic Acids Research 31: 7041–7055.

    Article  CAS  PubMed  Google Scholar 

  55. Besemer, J. and M. Borodovsky. 1999. Heuristic approach to deriving models for gene finding. Nucleic Acids Research 27:3911–3920.

    Article  CAS  PubMed  Google Scholar 

  56. Kattenhorn, L.M., R. Mills, M. Wagner, A. Lomsadze, V. Makeev, M. Borodovsky, H.L. Ploegh, B.M. Kessler, et al. 2004. Identification of proteins associated with murine cytomegalovirus virions. Journal of Virology 78:11187–11197.

    Article  CAS  PubMed  Google Scholar 

  57. Van Domselaar, G.H., P. Stothard, S. Shrivastava, J.A. Cruz, A. Guo, X. Dong, P. Lu, D. Szafron, et al. 2005. BASys: a web server for automated bacterial genome annotation. Nucleic Acids Research 33:W455–W459.

    Article  PubMed  Google Scholar 

  58. Delcher, A.L., D. Harmon, S. Kasif, O. White, and S.L. Salzberg. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Research 27:4636–4641.

    Article  CAS  PubMed  Google Scholar 

  59. Larsen, T.S. and A. Krogh. 2003. EasyGene – a prokaryotic gene finder that ranks ORFs by statistical significance. BMC Bioinformatics 4:21.

    Article  PubMed  Google Scholar 

  60. Bairoch, A., R. Apweiler, C.H. Wu, W.C. Barker, B. Boeckmann, S. Ferro, E. Gasteiger, H. Huang, et al. 2005. The Universal Protein Resource (UniProt). Nucleic Acids Research 33:D154–D159.

    Article  CAS  PubMed  Google Scholar 

  61. Bateman, A., L. Coin, R. Durbin, R.D. Finn, V. Hollich, S. Griffiths-Jones, A. Khanna, M. Marshall, et al. 2004. The Pfam protein families database. Nucleic Acids Research 32 Database issue:D138–D141.

    Google Scholar 

  62. Hulo, N., C.J. Sigrist, S. Le, V, P.S. Langendijk-Genevaux, L. Bordoli, A. Gattiker, C.E. De, P. Bucher, and A. Bairoch. 2004. Recent improvements to the PROSITE database. Nucleic Acids Research 32:D134–D137.

    Article  CAS  PubMed  Google Scholar 

  63. McGuffin, L.J., K. Bryson, and D.T. Jones. 2000. The PSIPRED protein structure prediction server. Bioinformatics 16:404–405.

    Article  CAS  PubMed  Google Scholar 

  64. Bocs, S., S. Cruveiller, D. Vallenet, G. Nuel, C. Medigue, S. Bocs, S. Cruveiller, D. Vallenet, et al. 2003. AMIGene: Annotation of MIcrobial Genes. Nucleic Acids Research 31: 3723–3726.

    Article  CAS  PubMed  Google Scholar 

  65. Yada, T. and M. Hirosawa. 1996. Detection of short protein coding regions within the cyanobacterium genome: application of the hidden Markov model. DNA Research 3:355–361.

    Article  CAS  PubMed  Google Scholar 

  66. Salzberg, S.L., A.L. Delcher, S. Kasif, and O. White. 1998. Microbial gene identification using interpolated Markov models. Nucleic Acids Research 26:544–548.

    Article  CAS  PubMed  Google Scholar 

  67. Ng, K.W., J. Lawson, H.R. Garner, K.w. Ng, J. Lawson, and H.R. Garner. 2004. PathoGene: a pathogen coding sequence discovery and analysis resource. BioTechniques 37:218–2.

    CAS  PubMed  Google Scholar 

  68. Altschul, S.F. and E.V. Koonin. 1998. Iterated profile searches with PSI-BLAST – a tool for discovery in protein databases. Trends in Biochemical Sciences 23:444–447.

    Article  CAS  PubMed  Google Scholar 

  69. Marchler-Bauer, A., J.B. Anderson, C. DeWeese-Scott, N.D. Fedorova, L.Y. Geer, S. He, D.I. Hurwitz, J.D. Jackson, et al. 2003. CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Research 31:383–387.

    Article  CAS  PubMed  Google Scholar 

  70. Letunic, I., R.R. Copley, S. Schmidt, F.D. Ciccarelli, T. Doerks, J. Schultz, C.P. Ponting, and P. Bork. 2004. SMART 4.0: towards genomic data integration. Nucleic Acids Research 32 Database issue:D142–D144.

    Google Scholar 

  71. Tatusov, R.L., N.D. Fedorova, J.D. Jackson, A.R. Jacobs, B. Kiryutin, E.V. Koonin, D.M. Krylov, R. Mazumder, et al. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41.

    Article  PubMed  Google Scholar 

  72. Quevillon, E., V. Silventoinen, S. Pillai, N. Harte, N. Mulder, R. Apweiler, and R. Lopez. 2005. InterProScan: protein domains identifier. Nucleic Acids Research 33:W116–W120.

    Article  CAS  PubMed  Google Scholar 

  73. Mulder, N.J., R. Apweiler, T.K. Attwood, A. Bairoch, A. Bateman, D. Binns, P. Bradley, P. Bork, et al. 2005. InterPro, progress and status in 2005. Nucleic Acids Research 33:D201–D205.

    Article  CAS  PubMed  Google Scholar 

  74. Sonnhammer, E.L.L., G. von Heijne, and A. Krogh. 1998. A hidden Markov model for predicting transmembrane helices in protein sequences., p. 175–182. In J. Glasgow, Littlejohn T., F. Major, R. Lathrop, D. Sankoff, and C. Sensen (Eds.), Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA.

    Google Scholar 

  75. Rey, S., M.Acab, J.L. Gardy, M.R. Laird, K. deFays, C. Lambert, and F.S. Brinkman. 2005. PSORTdb: a protein subcellular localization database for bacteria. Nucleic Acids Research 33:D164–D168.

    Article  CAS  PubMed  Google Scholar 

  76. Bendtsen, J.D., H. Nielsen, H.G. von, and S. Brunak. 2004. Improved prediction of signal peptides: SignalP 3.0. Journal of Molecular Biology 340:783–795.

    Article  PubMed  Google Scholar 

  77. Carver, T.J., K.M. Rutherford, M. Berriman, M.-A. Rajandream, B.G. Barrell, and J. Parkhill. 2005. ACT: the Artemis comparison tool. Bioinformatics 21:3422–3423.

    Article  CAS  PubMed  Google Scholar 

  78. Darling, A.C., B. Mau, F.R. Blattner, and N.T. Perna. 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Research 14:1394–1403.

    Article  CAS  PubMed  Google Scholar 

  79. Zafar, N., R.Mazumder, and D. Seto. 2002. CoreGenes: a computational tool for identifying and cataloging “core” genes in a set of small genomes. BMC Bioinformatics 3:12.

    Article  PubMed  Google Scholar 

  80. Celamkoti, S., S. Kundeti, A. Purkayastha, R. Mazumder, C. Buck, and D. Seto. 2004. GeneOrder3.0: software for comparing the order of genes in pairs of small bacterial genomes. BMC Bioinformatics 5:52.

    Article  PubMed  Google Scholar 

  81. Schwartz, S., Z. Zhang, K.A. Frazer, A. Smit, C. Riemer, J. Bouck, R. Gibbs, R. Hardison, and W. Miller. 2000. PipMaker – a web server for aligning two genomic DNA sequences. Genome Research 10:577–586.

    Article  CAS  PubMed  Google Scholar 

  82. Ovcharenko, I., G.G. Loots, R.C. Hardison, W. Miller, and L. Stubbs. 2004. zPicture: dynamic alignment and visualization tool for analyzing conservation profiles. Genome Research 14:472–477.

    Article  CAS  PubMed  Google Scholar 

  83. Loots, G.G. and I. Ovcharenko. 2004. rVISTA 2.0: evolutionary analysis of transcription factor binding sites. Nucleic Acids Research 32:W217–W221.

    Article  CAS  PubMed  Google Scholar 

  84. Abbott, J.C., D.M. Aanensen, K. Rutherford, S. Butcher, and B. G. Spratt. 2005. WebACT – an online companion for the Artemis Comparison Tool. Bioinformatics 21: 3665–3666.

    Article  CAS  PubMed  Google Scholar 

  85. Kwan, T., J. Liu, M. DuBow, P. Gros, and J. Pelletier. 2005. The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages. Proceedings of the National Academy of Sciences of the United States of America 102:5174–5179.

    Article  CAS  PubMed  Google Scholar 

  86. Lord, P.W., J.N. Selley, and T.K. Attwood. 2002. CINEMA-MX: a modular multiple alignment editor. Bioinformatics 18:1402–1403.

    Article  CAS  PubMed  Google Scholar 

  87. Mazumder, R., A. Kolaskar, and D. Seto. 2001. GeneOrder: comparing the order of genes in small genomes. Bioinformatics 17:162–166.

    Article  CAS  PubMed  Google Scholar 

  88. Cerdeno-Tarraga, A.M., S. Patrick, L.C. Crossman, G. Blakely, V. Abratt, N. Lennard, I. Poxton, B. Duerden, et al. 2005. Extensive DNA inversions in the B. fragilis genome control variable gene expression. Science 307:1463–1465.

    Article  CAS  PubMed  Google Scholar 

  89. Cerdeno-Tarraga, A.M., A. Efstratiou, L.G. Dover, M.T. Holden, M. Pallen, S.D. Bentley, G.S. Besra, C. Churcher, et al. 2003. The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129. Nucleic Acids Research 31:6516–6523.

    Article  CAS  PubMed  Google Scholar 

  90. Parkhill, J., M. Sebaihia, A. Preston, L.D. Murphy, N. Thomson, D.E. Harris, M.T. Holden, C.M. Churcher, et al. 2003. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nature Genetics 35:32–40.

    Article  PubMed  Google Scholar 

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Author information

Authors and Affiliations

  1. Public Health Agency of Canada, Laboratory for Foodborne Diseases, Guelph, Ontario, Canada

    Andrew M. Kropinski

  2. Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada

    Andrew M. Kropinski

  3. Department of Microbiology, Immunology Queen’s University, Kingston, Ontario, Canada

    Andrew M. Kropinski

  4. Wallace H. Coulter Department of Biomedical Engineering and Division of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA, USA

    Mark Borodovsky

  5. Wellcome Trust Genome Campus, Sulston Laboratories, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK

    Tim J. Carver

  6. Wellcome Trust Genome Campus, Sulston Laboratories, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK

    Ana M. Cerdeño-Tárraga

  7. University of Wisconsin-Madison, Madison, WI, USA

    Aaron Darling

  8. Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA

    Alexandre Lomsadze

  9. Department of Bioinformatics and Computational Biology, George Mason University, Manassas, VA, USA

    Padmanabhan Mahadevan

  10. Department of Biological Sciences, Biological Sciences Centre, University of Alberta, Edmonton, Alberta, Canada

    Paul Stothard

  11. Department of Bioinformatics and Computational Biology, George Mason University, Manassas, VA, USA

    Donald Seto

  12. National Microbiology Laboratory, Canadian Science Centre for Human and Animal Health, Winnipeg, Manitoba, Canada

    Gary Van Domselaar

  13. Department of Computing Science and Biological Sciences, National Institute for Nanotechnology, University of Alberta, Edmonton, Alberta, Canada

    David S. Wishart

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  1. Andrew M. Kropinski
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  6. Alexandre Lomsadze
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Editor information

Editors and Affiliations

  1. University of Leicester, Leicester, UK

    Martha R.J. Clokie

  2. Public Health Agency of Canada, Guelph, Ontario, Canada

    Andrew M. Kropinski

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© 2009 Humana Press, a part of Springer Science+Business Media, LLC

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Kropinski, A.M. et al. (2009). In Sffamily Identification of Genes in Bacteriophage DNA. In: Clokie, M.R., Kropinski, A.M. (eds) Bacteriophages. Methods in Molecular Biology™, vol 502. Humana Press. https://doi.org/10.1007/978-1-60327-565-1_6

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  • DOI: https://doi.org/10.1007/978-1-60327-565-1_6

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60327-564-4

  • Online ISBN: 978-1-60327-565-1

  • eBook Packages: Springer Protocols

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