The adaptation of temperate bacteriophages to their host genomes

Molecular Biology and Evolution

Volumn 30, Issue 4, 2013, Pages 737-751

  Bobay, Louis Marie ^a,b,c   Rocha, Eduardo P C ^a,b   Touchon, Marie ^a,b  

^a INSTITUT PASTEUR   (France)

^b CNRS   (France)

^c SORBONNE UNIVERSITÉ   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIOPHAGE; CHROMOSOME SEGREGATION; CHROMOSOME STRUCTURE; ESCHERICHIA COLI; EVOLUTIONARY ADAPTATION; GENE EXPRESSION; LYSOGENIZATION; NONHUMAN; PROPHAGE; PROTEIN MOTIF; PURIFYING SELECTION; SALMONELLA ENTERICA;

ADAPTATION, BIOLOGICAL; CHROMOSOME MAPPING; CHROMOSOMES, BACTERIAL; COLIPHAGES; ESCHERICHIA COLI; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOME, BACTERIAL; LIKELIHOOD FUNCTIONS; LYSOGENY; PHYLOGENY; PROPHAGES; SALMONELLA ENTERICA; SALMONELLA PHAGES; VIRAL TROPISM;

BACTERIA (MICROORGANISMS); ESCHERICHIA; SALMONELLA;

EID: 84875582587     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mss279     Document Type: Article

References (123)

1. Abedon ST, Calendar RL. 2005. The bacteriophages. New York: Oxford University Press..
2. Abedon ST, Lejeune JT. 2005. Why bacteriophage encode exotoxins and other virulence factors. Evol Bioinform Online. 1:97-110..
3. Ackermann HW. 2007. Salmonella phages examined in the electron microscope. Methods Mol Biol. 394:213-234..
4. Allison GE, Angeles D, Tran-Dinh N, Verma NK. 2002. Complete genomic sequence of SfV, a serotype-converting temperate bacteriophage of Shigella flexneri. J Bacteriol. 184:1974-1987..
5. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402..
6. Angly FE, Felts B, Breitbart M, et al. (18 co-authors). 2006. The marine viromes of four oceanic regions. PLoS Biol. 4:e368..
7. Asadulghani M, Ogura Y, Ooka T, Itoh T, Sawaguchi A, Iguchi A, Nakayama K, Hayashi T. 2009. The defective prophage pool of Escherichia coli O157: prophage-prophage interactions potentiate horizontal transfer of virulence determinants. PLoS Pathog. 5: e1000408..
8. Baba T, Ara T, HasegawaM, Takai Y, Okumura Y, BabaM, Datsenko KA, Tomita M, Wanner BL, Mori H. 2006. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol. 2:2006.0008..
9. Balbontin R, Figueroa-Bossi N, Casadesus J, Bossi L. 2008. Insertion hot spot for horizontally acquired DNA within a bidirectional small-RNA locus in Salmonella enterica. J Bacteriol. 190:4075-4078..
10. Banks DJ, Beres SB, Musser JM. 2002. The fundamental contribution of phages to GAS evolution, genome diversification and strain emergence. Trends Microbiol. 10:515-521..
11. Bigot S, Saleh OA, Lesterlin C, Pages C, El Karoui M, Dennis C, Grigoriev M, Allemand JF, Barre FX, Cornet F. 2005. KOPS: DNA motifs that control E. coli chromosome segregation by orienting the FtsK translocase. EMBO J. 24:3770-3780..
12. Blum G, Ott M, Lischewski A, Ritter A, Imrich H, Tschape H, Hacker J. 1994. Excision of large DNA regions termed pathogenicity islands from tRNA-specific loci in the chromosome of an Escherichia coli wild-type pathogen. Infect Immun. 62:606-614..
13. Bossi L, Fuentes JA, Mora G, Figueroa-Bossi N. 2003. Prophage contribution to bacterial population dynamics. J Bacteriol. 185:6467-6471..
14. Botstein D. 1980. A theory ofmodular evolution for bacteriophages. Ann N Y Acad Sci. 354:484-490..
15. Boyd EF, Brussow H. 2002. Common themes among bacteriophageencoded virulence factors and diversity among the bacteriophages involved. Trends Microbiol. 10:521-529..
16. Breitbart M, Haynes M, Kelley S, et al. (13 co-authors). 2008. Viral diversity and dynamics in an infant gut. Res Microbiol. 159:367-373..
17. Brown SP, Le Chat L, De Paepe M, Taddei F. 2006. Ecology of microbial invasions: amplification allows virus carriers to invade more rapidly when rare. Curr Biol. 16:2048-2052..
18. Brussow H, Canchaya C, Hardt WD. 2004. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol Mol Biol Rev. 68:560-602..
19. Bukhari AI, Metlay M. 1973. Genetic mapping of prophage Mu. Virology 54:109-116..
20. Campbell A. 2003. Prophage insertion sites. Res Microbiol. 154:277-282..
21. Campbell A, Botstein D. 1983. Evolution of the lambdoid phages. In: Hendrix RW, Roberts JW, Stahl FW, Weisberg RA, editors. Lambda II. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory. p. 365-380..
22. Campbell AM. 1992. Chromosomal insertion sites for phages and plasmids. J Bacteriol. 174:7495-7499..
23. Campbell AM. 2002. Preferential orientation of natural lambdoid prophages and bacterial chromosome organization. Theor Popul Biol. 61:503-507..
24. Canchaya C, Fournous G, Brussow H. 2004. The impact of prophages on bacterial chromosomes. Mol Microbiol. 53:9-18..
25. Canchaya C, Proux C, Fournoux G, Bruttin A, Brussow H. 2003. Prophage genomics. Microbiol Mol Biol Rev. 67:238-276..
26. Casjens S. 2003. Prophages and bacterial genomics: what have we learned so far? Mol Microbiol. 49:277-300..
27. Couturier E, Rocha EPC. 2006. Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes. Mol Microbiol. 59: 1506-1518..
28. Creuzburg K, Heeren S, Lis CM, Kranz M, Hensel M, Schmidt H. 2011. Genetic background and mobility of variants of the gene nleA in attaching and effacing Escherichia coli. Appl Environ Microbiol. 77: 8705-8713..
29. Criscuolo A, Gribaldo S. 2010. BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol. 10: 210..
30. Cui T, Moro-oka N, Ohsumi K, Kodama K, Ohshima T, Ogasawara N, Mori H, Wanner B, Niki H, Horiuchi T. 2007. Escherichia coli with a linear genome. EMBO Rep. 8:181-187..
31. Dearborn AD, Laurinmaki P, Chandramouli P, Rodenburg CM, Wang S, Butcher SJ, Dokland T. 2012. Structure and size determination of bacteriophage P2 and P4 procapsids: function of size responsiveness mutations. J Struct Biol. 178:215-224..
32. Dobrindt U, Blum-Oehler G, Nagy G, Schneider G, Johann A, Gottschalk G, Hacker J. 2002. Genetic structure and distribution of four pathogenicity islands (PAI I(536) to PAI IV(536)) of uropathogenic Escherichia coli strain 536. Infect Immun. 70:6365-6372..
33. Dong H, Nilsson L, Kurland CG. 1996. Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J Mol Biol. 260:649-663..
34. Duggin IG, Bell SD. 2009. Termination structures in the Escherichia coli chromosome replication fork trap. J Mol Biol. 387:532-539..
35. Eddy SR. 2011. Accelerated profile HMM searches. PLoS Comput Biol. 7: e1002195..
36. Edgar R, Rokney A, Feeney M, Semsey S, Kessel M, Goldberg MB, Adhya S, Oppenheim AB. 2008. Bacteriophage infection is targeted to cellular poles. Mol Microbiol. 68:1107-1116..
37. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797..
38. Edlin G, Lin L, Bitner R. 1977. Reproductive fitness of P1, P2, and Mu lysogens of Escherichia coli. J Virol. 21:560-564..
39. Edwards RA, Rohwer F. 2005. Viral metagenomics. Nat Rev Microbiol. 3: 504-510..
40. Esnault E, ValensM, Espeli O, Boccard F. 2007. Chromosome structuring limits genome plasticity in Escherichia coli. PLoS Genet. 3:e226..
41. Fouts DE. 2006. Phage-Finder: automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res. 34:5839-5851..
42. Garcia-Aljaro C, Muniesa M, Jofre J, Blanch AR. 2009. Genotypic and phenotypic diversity among induced, stx2-carrying bacteriophages from environmental Escherichia coli strains. Appl Environ Microbiol. 75:329-336..
43. Garcia-Russell N, Harmon TG, Le TQ, Amaladas NH, Mathewson RD, Segall AM. 2004. Unequal access of chromosomal regions to each other in Salmonella: probing chromosome structure with phage lambda integrase-mediated long-range rearrangements. Mol Microbiol. 52:329-344..
44. Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol. 14:685-695..
45. Greub G, Mege JL, Raoult D. 2003. Parachlamydia acanthamoebae enters and multiplies within human macrophages and induces their apoptosis. Infect Immun. 71:5979-5985..
46. Gruber AR, Lorenz R, Bernhart SH, Neubock R, Hofacker IL. 2008. The Vienna RNA websuite. Nucleic Acids Res. 36:W70-W74..
47. Guerrero-Ferreira RC, Viollier PH, Ely B, Poindexter JS, Georgieva M, Jensen GJ, Wright ER. 2011. Alternative mechanism for bacteriophage adsorption to the motile bacterium Caulobacter crescentus. Proc Natl Acad Sci U S A. 108:9963-9968..
48. Hendrickson H, Lawrence JG. 2007. Mutational bias suggests that replication termination occurs near the dif site, not at Ter sites. Mol Microbiol. 64:42-56..
49. Hendrix RW, Smith MCM, Burns RN, Ford ME, Hatfull GF. 1999. Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage. Proc Natl Acad Sci U S A. 96: 2192-2197..
50. Hermans AP, Beuling AM, van Hoek AH, Aarts HJ, Abee T, Zwietering MH. 2006. Distribution of prophages and SGI-1 antibiotic-resistance genes among different Salmonella enterica serovar Typhimurium isolates. Microbiology 152:2137-2147..
51. Huang HY, Chang HY, Chou CH, Tseng CP, Ho SY, Yang CD, Ju YW, Huang HD. 2009. sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes. Nucleic Acids Res. 37:D150-D154..
52. Huber KE, Waldor MK. 2002. Filamentous phage integration requires the host recombinases XerC and XerD. Nature 417:656-659..
53. ItayaM, Tsuge K, KoizumiM, Fujita K. 2005. Combining two genomes in one cell: stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome. Proc Natl Acad Sci U S A. 102: 15971-15976..
54. Jobb G, von Haeseler A, Strimmer K. 2004. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol. 4:18..
55. Juhala RJ, Ford ME, Duda RL, Youlton A, Hatfull GF, Hendrix RW. 2000. Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages. J Mol Biol. 299: 27-51..
56. Julio SM, Heithoff DM, Mahan MJ. 2000. ssrA (tmRNA) plays a role in Salmonella enterica serovar Typhimurium pathogenesis. J Bacteriol. 182:1558-1563..
57. King AMQ, Lefkowitz E, Adams MJ, Carstens EB. 2011. Virus taxonomy: ninth report of the International Committee on Taxonomy of Viruses. Waltham (MA): Elsevier.
58. Kourilsky P. 1973. Lysogenization by bacteriophage lambda. I. Multiple infection and the lysogenic response. Mol Gen Genet. 122:183-195..
59. Kroger C, Dillon SC, Cameron AD, et al. (21 co-authors). 2012. The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium. Proc Natl Acad Sci U S A. 109: E1277-E1286..
60. Labrie SJ, Samson JE, Moineau S. 2010. Bacteriophage resistance mechanisms. Nat Rev Microbiol. 8:317-327..
61. Lathe WC, Snel B, Bork P. 2000. Gene context conservation of a higher order than operons. Trends Biochem Sci. 25:474-479..
62. Lavigne R, Darius P, Summer EJ, Seto D, Mahadevan P, Nilsson AS, Ackermann HW, Kropinski AM. 2009. Classification of Myoviridae bacteriophages using protein sequence similarity. BMC Microbiol. 9: 224..
63. Lawrence JG, Hendrickson H. 2003. Lateral gene transfer: when will adolescence end? Mol Microbiol. 50:739-749..
64. Lee SY, Bailey SC, Apirion D. 1978. Small stable RNAs from Escherichia coli: evidence for the existence of new molecules and for a new ribonucleoprotein particle containing 6S RNA. J Bacteriol. 133: 1015-1023..
65. Levy O, Ptacin JL, Pease PJ, Gore J, Eisen MB, Bustamante C, Cozzarelli NR. 2005. Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocase. Proc Natl Acad Sci U S A. 102:17618-17623..
66. Lima-Mendez G, Van Helden J, Toussaint A, Leplae R. 2008a. Prophinder: a computational tool for prophage prediction in prokaryotic genomes. Bioinformatics 24:863-865..
67. Lima-Mendez G, Van Helden J, Toussaint A, Leplae R. 2008b. Reticulate representation of evolutionary and functional relationships between phage genomes. Mol Biol Evol. 25:762-777..
68. Lowe T, Eddy S. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964..
69. Mackiewicz P, Zakrzewska-Czerwinska J, Zawilak A, DudekMR, Cebrat S. 2004. Where does bacterial replication start? Rules for predicting the oriC region. Nucleic Acids Res. 32:3781-3791..
70. McDaniel TK, Jarvis KG, DonnenbergMS, Kaper JB. 1995. A genetic locus of enterocyte effacement conserved among diverse enterobacterial pathogens. Proc Natl Acad Sci U S A. 92:1664-1668..
71. Meile JC, Mercier R, Stouf M, Pages C, Bouet JY, Cornet F. 2011. The terminal region of the E. coli chromosome localises at the periphery of the nucleoid. BMC Microbiol. 11:28..
72. Mercier R, Petit MA, Schbath S, Robin S, El KarouiM, Boccard F, Espeli O. 2008. The MatP/matS site-specific system organizes the terminus region of the E. coli chromosome into a macrodomain. Cell 135: 475-485..
73. Mizuuchi K. 1992. Transpositional recombination: mechanistic insights from studies of Mu and other elements. Annu Rev Biochem. 61: 1011-1051..
74. Mmolawa PT, Schmieger H, Heuzenroeder MW. 2003. Bacteriophage ST64B, a genetic mosaic of genes from diverse sources isolated from Salmonella enterica serovar typhimurium DT 64. J Bacteriol. 185: 6481-6485..
75. Napolitano MG, Almagro-Moreno S, Boyd EF. 2011. Dichotomy in the evolution of pathogenicity island and bacteriophage encoded integrases from pathogenic Escherichia coli strains. Infect Genet Evol. 11:423-436..
76. Nechaev S, Severinov K. 2008. The elusive object of desire-interactions of bacteriophages and their hosts. Curr Opin Microbiol. 11: 186-193..
77. Nunes-Duby SE, Kwon HJ, Tirumalai RS, Ellenberger T, Landy A. 1998. Similarities and differences among 105 members of the Int family of site-specific recombinases. Nucleic Acids Res. 26:391-406..
78. Ohnishi M, Kurokawa K, Hayashi T. 2001. Diversification of Escherichia coli genomes: are bacteriophages the major contributors? Trends Microbiol. 9:481-485..
79. Otsuka AJ, Buoncristiani MR, Howard PK, Flamm J, Johnson C, Yamamoto R, Uchida K, Cook C, Ruppert J, Matsuzaki J. 1988. The Escherichia coli biotin biosynthetic enzyme sequences predicted from the nucleotide sequence of the bio operon. J Biol Chem. 263: 19577-19585.
80. Peters JE, Craig NL. 2001. Tn7 recognizes transposition target structures associated with DNA replication using the DNA-binding protein TnsE. Genes Dev. 15:737-747..
81. Ptashne M. 1992. Genetic switch: phage lambda and higher organisms. Cambridge (MA): Blackwell.
82. Raghavan R, Groisman EA, Ochman H. 2011. Genome-wide detection of novel regulatory RNAs in E. coli. Genome Res. 21: 1487-1497..
83. Ravin NV. 2011. N15: the linear phage-plasmid. Plasmid 65:102-109..
84. Reyes A, HaynesM, Hanson N, Angly FE, Heath AC, Rohwer F, Gordon JI. 2010. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466:334-338..
85. Reyes-Lamothe R, Wang X, Sherratt D. 2008. Escherichia coli and its chromosome. Trends Microbiol. 16:238-245..
86. Rice P, Longden I, Bleasby A. 2000. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 16:276-277..
87. Rocha EPC. 2004. Order and disorder in bacterial genomes. Curr Opin Microbiol. 7:519-527..
88. Rocha EPC. 2008. The organisation of the bacterial genome. Annu Rev Genet. 42:211-233..
89. Rocha EPC, Danchin A. 2003. Essentiality, not expressiveness, drives gene strand bias in bacteria. Nat Genet. 34:377-378..
90. Rohwer F, Edwards R. 2002. The phage proteomic tree: a genome-based taxonomy for phage. J Bacteriol. 184:4529-4535..
91. Roossinck MJ. 2011. The good viruses: viral mutualistic symbioses. Nat Rev Microbiol. 9:99-108..
92. Schbath S. 1997. An efficient statistic to detect over- and underrepresented words in DNA sequences. J Comput Biol. 4:189-192..
93. Schmidt HA, Strimmer K, Vingron M, von Haeseler A. 2002. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504..
94. Scolari VF, Bassetti B, Sclavi B, Lagomarsino MC. 2011. Gene clusters reflecting macrodomain structure respond to nucleoid perturbations. Mol Biosyst. 7:878-888..
95. Shinedling S, Parma D, Gold L. 1987. Wild-type bacteriophage T4 is restricted by the lambda rex genes. J Virol. 61:3790-3794..
96. Shinhara A, Matsui M, Hiraoka K, Nomura W, Hirano R, Nakahigashi K, Tomita M, Mori H, Kanai A. 2011. Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli. BMC Genomics 12:428..
97. Six EW, Klug CA. 1973. Bacteriophage P4: a satellite virus depending on a helper such as prophage P2. Virology 51:327-344..
98. Smith MC, Thorpe HM. 2002. Diversity in the serine recombinases. Mol Microbiol. 44:299-307..
99. Snel B, Huynen MA, Dutilh BE. 2005. Genome trees and the nature of genome evolution. Ann Rev Microbiol. 59:191-209..
100. St-Pierre F, Endy D. 2008. Determination of cell fate selection during phage lambda infection. Proc Natl Acad Sci U S A. 105:20705-20710..
101. Suttle CA. 2005. Viruses in the sea. Nature 437:356-361..
102. Tenaillon O, Skurnik D, Picard B, Denamur E. 2010. The population genetics of commensal Escherichia coli. Nat Rev Microbiol. 8:207-17..
103. Thomson N, Baker S, Pickard D, et al. (15 co-authors). 2004. The role of prophage-like elements in the diversity of Salmonella enterica serovars. J Mol Biol. 339:279-300..
104. Touchon M, Hoede C, Tenaillon O, et al. (41 co-authors). 2009. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet. 5:e1000344..
105. Touchon M, Rocha EP. 2007. Causes of insertion sequences abundance in prokaryotic genomes. Mol Biol Evol. 24:969-981..
106. TouchonM, Rocha EP. 2010. The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella. PLoS One 5:e11126..
107. Touzain F, Petit MA, Schbath S, El Karoui M. 2011. DNA motifs that sculpt the bacterial chromosome. Nat Rev Microbiol. 9:15-26..
108. Val ME, Skovgaard O, Ducos-Galand M, Bland MJ, Mazel D. 2012. Genome engineering in Vibrio cholerae: a feasible approach to address biological issues. PLoS Genet. 8:e1002472..
109. Valens M, Penaud S, Rossignol M, Cornet F, Boccard F. 2004. Macrodomain organization of the Escherichia coli chromosome. EMBO J. 23:4330-4341..
110. Van Melderen L, Saavedra De Bast M. 2009. Bacterial toxin-antitoxin systems: more than selfish entities? PLoS Genet. 5:e1000437..
111. Vernikos GS, Thomson NR, Parkhill J. 2007. Genetic flux over time in the Salmonella lineage. Genome Biol. 8:R100..
112. Wang H, Yang CH, Lee G, Chang F,Wilson H, del Campillo-Campbell A, Campbell A. 1997. Integration specificities of two lambdoid phages (21 and e14) that insert at the same attB site. J Bacteriol. 179: 5705-5711..
113. Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S. 2001. Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev. 15:1637-1651.
114. Waters LS, Storz G. 2009. Regulatory RNAs in bacteria. Cell 136:615-628..
115. Weinbauer MG. 2004. Ecology of prokaryotic viruses. FEMS Microbiol Rev. 28:127-181..
116. Wiggins PA, Cheveralls KC, Martin JS, Lintner R, Kondev J. 2010. Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament. Proc Natl Acad Sci U S A. 107:4991-4995..
117. Williams KP. 2002. Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies. Nucleic Acids Res. 30:866-875.
118. Williams KP. 2003. Traffic at the tmRNA gene. J Bacteriol. 185: 1059-1070..
119. Winstanley C, Langille MGI, Fothergill JL, et al. (19 co-authors). 2008. Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa. Genome Res. 19:12-23..
120. Withers M, Wernisch L, dos Reis M. 2006. Archaeology and evolution of transfer RNA genes in the Escherichia coli genome. RNA 12: 933-942..
121. Wolf YI, Rogozin IB, Grishin NV, Koonin EV. 2002. Genome trees and the tree of life. Trends Genet. 18:472-479..
122. Zaslaver A, Mayo A, Ronen M, Alon U. 2006. Optimal gene partition into operons correlates with gene functional order. Phys Biol. 3: 183-189..
123. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. 2011. PHAST: a fast phage search tool. Nucleic Acids Res. 39:W347-W352..