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[1] A Rajeev K. Azad and Jeffrey G. Lawrence. Use of artificial geonmes in assessing methods for atypical gene detection. PLoS Comput Biol, 1(5), November 2005.
[2] Claire Balding, Stephen A. Bromley, Roger W. Pickup, and Jon R. Saunders. Diversity of phage integrases in enterobacteriaceae: development of markers for environmental analysis of temperate phages. Environmental Microbiology, 7(10):1558-1567, October 2005.
[3] Samuel Baron, editor. Medical Microbiology. The University of Texas Medical Branch at Galveston, fourth edition, 1996.
[4] Michael Bose and Robert D. Barber. Prophage finder: a prophage loci prediction tool for prokaryotic genome sequences. In Silico Biol, 6(3), April 2006.
[5] H. Brussow, C. Canchaya, and W.D. Hardt. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol Mol Biol Rev, 68(3):560-602, September 2004.
[6] Frederic Bushman. Lateral DNA Transfer: Mechanisms and Consequences. Cold Spring Harbor Laboratory Press, November 2001.
[7] A. Campbell. Prophage insertion sites. Res Microbiol, 154(4):277-282, May 2003.
[8] A.M. Campbell. Chromosomal insertion sites for phages and plasmids. J Bacteriol, 174(23):7495-7499, December 1992.
[9] Carlos Canchaya, Ghislain Fournous, and Harald Brussow. The impact of prophages on bacterial chromosomes. Molecular Microbiology, 32(1):9-18, July 2004.
[10] Carlos Canchaya, Caroline Proux, Ghislain Fournous, Anne Bruttin, and Harald Brussow. Prophage genomics. Microbiology and Molecular Biology Reviews, 67(2):238-276, June 2003.
[11] S.R. Casjens. Comparative genomics and evolution of the tail-bacteriophages. Curr Opin Microbiol, 8(4):451-458, August 2005.
[12] Ines Chen, Peter J. Christie, and David Dubnau. The ins and outs of dna transfer in bacteria. Science, 310(5753):1456-1460, December 2005.
[13] S.R. Eddy and R. Durbin. Rna sequence analysis using covariance models. Nucleic Acids Res, 22(11):2079-2088, June 1994.
[14] Robert A. Edwards and Forest Rohwer. Opinion: Viral metagenomics. Nature Reviews Microbiology, 3(6):504-510, June 1994.
[15] Andrew E. Firth and Chris M. Brown. Detecting overlapping coding sequences in virus genomes. BMC Bioinformatics, 7(1), February 2006.
[16] Patrick Forterre. The origin of viruses and their possible roles in major evolutionary transitions. Virus Research, 117(1):5-16, April 2006.
[17] Derrick E. Fouts. Phage_finder: Automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res, October 2006.
[18] Amy C. Groth and Michele P. Calos. Phage integrases: Biology and applications. Journal of Molecular Biology, 335(3):667-678, January 2004.
[19] M.A. Hauser and J.J. Scocca. Site-specific integration of the haemophilus influenzae bacteriophage hp1: location of the boundaries of the phage attachment site. J Bacteriol, 174(20):6674-6677, October 1992.
[20] T. Hayashi, K. Makino, M. Ohnishi, K. Kurokawa, K. Ishii, K. Yokoyama, C.G. Han, E. Ohtsubo, K. Nakayama, T. Murata, M. Tanaka, T. Tobe, T. Iida, H. Takami, T. Honda, C. Sasakawa, N. Ogasawara, T. Yasunaga, S. Kuhara, T. Shiba, M. Hattori, and H. Shinagawa. Complete genome sequence of enterohemorrhagic escherichia coli o157:h7 and genomic comparison with a laboratory strain k-12. DNA Res, 8(1):11-22, February 2001.
[21] A.P. Hermans, A.M. Beuling, A.H. van Hoek, H.J. Aarts, T. Abee, and M.H. Zwietering. Distribution of prophages and sgi-1 antibiotic-resistance genes among different salmonella enterica serovar typhimurium isolates. Microbiology, 152(Pt 7):2137-2147, July 2006.
[22] W. Hsiao, I. Wan, S.J. Jones, and F.S. Brinkman. Islandpath: aiding detection of genomic islands in prokaryotes. Bioinformatics, 19(3):418-420, February 2003.
[23] P. Lauer, M.Y. Chow, M.J. Loessner, D.A. Portnoy, and R. Calendar. Construction, characterization, and use of two listeria monocytogenes site-specific phage integration vectors. J Bacteriol, 184(15):4177-4186, August 2002.
[24] R. Leplae, A. Hebrant, S.J. Wodak, and A. Toussaint. Aclame: a classification of mobile genetic elements. Nucleic Acids Res, 32(Database issue), January 2004.
[25] T.M. Lowe and S.R. Eddy. trnascan-se: a program for improved detection of transfer rna genes in genomic sequence. Nucleic Acids Res, 25(5):955-964, March 1997.
[26] Y. Mantri and K.P. Williams. Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their dna site specificites. Nucleic Acids Res, 32(Database issue), January 2004.
[27] Ian J. Molineux. Fifty-three years since hershey and chase; much ado about pressure but which pressure is it? Virology, 344(1):221-229, January 2006.
[28] Daniel Nelson. Phage taxonomy: We agree to disagree. J Bacteriol, 186(21):7029-7031, November 2004.
[29] H.Y. Ou, L.L. Chen, J. Lonnen, R.R. Chaudhuri, A.B. Thani, R. Smith, N.J. Garton, J. Hinton, M. Pallen, M.R. Barer, and K. Rajakumar. A novel strategry for the indentification of genomic islands by comparative analysis of the contents and contexts of trna sites in closely related bacteria. Nucleic Acids Res, 34(1), 2006.
[30] R. Ravatn, S. Studer, A.J. Zehnder, and J.R. van der Meer. Int-b13, an unusual site-specific recombinase of the bacteriophage p4 integrase family, is responsible for chromosomal insertion of the 105-kilobase clc element of pseudomonas sp. strain b13. J Bacteriol, 180(21):5505-5514, November 1998.
[31] W.D. Reiter, P.Palm, and S. Yeats. Transfer rna genes frequently serve as integration sites for prokaryotic genetic elements. Nucleic Acids Res, 17(5):1907-1914, March 1989.
[32] Edit Rutkai, Andrea Gyorgy, Laszlo Dorgai, and Robert A. Weisberg. Role of secondary attachment sites in changing the specificity of site-specific recombination. J Bacteriol, 188(9):3409-3411, May 2006.
[33] Soren J. Sorensen, Mark Bailey, Lars H. Hansen, Niels Kroer, and Stefan Wuertz. Studying plasmid horizontal transfer in situ: A critical review. Nat Rev Micro, 3(9):700-710, 2005.
[34] M. Sprinzl and K.W. Vassilenko. Compilation of trna sequences and sequences of trna genes. Nucleic Acids Res, 33(Database issue), January 2005.
[35] Christopher M. Thomas and Kaare M. Nielsen. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nature Reviews Microbiology, 3(9):711-721, September 2005.
[36] C.R. Tinsley, E. Bille, and X. Nassif. Bacteriophages and pathogenicity: more than just providing a toxin? Microbes Infect, 8(5):1365-1371, April 2006.
[37] M.H. Van Regenmortel, International and C.M. Fauquet. Virus Taxonomy: Classification and Nomenclature of Viruses: Seventh Report of the International Committee on Taxonomy of Viruses. Academic Press, October 2000.
[38] M. Ventura, C. Canchaya, D. Pridmore, B. Berger, and H. Brussow. Integration and distribution of lactobacillus johnsonii prophages. J Bacteriol, 185(15):4603-4608, August, 2003.
[39] S. Waack, O. Keller, R. Asper, T. Brodag, C. Damm, W.F. Fricke, K. Surovcik, P. Meinicke, and R. Merkl. Score-based prediction of genomic islands in prokaryotic genomes using hidden markov models. BMC Bioinformatics, 7, 2006.
[40] K.P. Williams. Integration sites for genetic elements in prokaryotic trna and tmran genes: sublocation preference of integrase subfamilies. Nucleic Acids Res, 30(4):866-875, February 2002.
[41] R.M. Woodsmall and D.A. Benson. Information resources at the national center for biotechnology information. Bull Med Libr Assoc, 81(3):282-284, July 1993.
[42] K. Yokoyama, K. Makino, Y. Kubota, M. Watanabe, S. Kimura, C.H. Yutsudo, K. Kurokawa, K. Ishii, M. Hattori, I. Tatsuno, H. Abe, M. Yoh, T. Iida, M. Ohnishi, T. Hayashi, T. Yasunaga, T. Honda, C. Sasakawa, and H. Shinagawa. Complete nucleotide sequence of the prophage vt1-sakai carrying the shiga toxin 1 genes of the enterohemorrhagic escherichia coli o157:h7 strain derived from the sakai outbreak. Gene, 258(1-2):127-139, November 2000.
[43] S.H. Yoon, C.G. Hur, H.Y. Kang, Y.H. Kim, T.K. Oh, and J.F. Kim. A computational approach for identifying pathogenicity islands in prokaryotic genomes. BMC Bioinformatics, 6, 2005.
[44] M. Zuker. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res, 31(13):3406-3415, July 2003.