publication . Article . 2012

PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

Ramy K. Aziz; Sajia Akhter; Robert Edwards;
Open Access
  • Published: 14 May 2012
Abstract
Prophages are phages in lysogeny that are integrated into, and replicated as part of, the host bacterial genome. These mobile elements can have tremendous impact on their bacterial hosts’ genomes and phenotypes, which may lead to strain emergence and diversification, increased virulence or antibiotic resistance. However, finding prophages in microbial genomes remains a problem with no definitive solution. The majority of existing tools rely on detecting genomic regions enriched in protein-coding genes with known phage homologs, which hinders the de novo discovery of phage regions. In this study, a weighted phage detection algorithm, PhiSpy was developed based on...
Subjects
Medical Subject Headings: viruses
free text keywords: Methods Online, Genetics, Prophage, Biology, GC skew, Bacterial genome size, Genome, Gene, Temperateness, Mobile genetic elements, Lysogenic cycle, Algorithm
Funded by
NSF| Collaborative Research: PHANTOME: PHage ANnotation TOols and MEthods
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0850356
  • Funding stream: Directorate for Biological Sciences | Division of Biological Infrastructure
55 references, page 1 of 4

Casjens, S. Prophages and bacterial genomics: what have we learned so far?. Mol. Microbiol.. 2003; 49: 277-300 [OpenAIRE] [PubMed]

Casjens, S, Palmer, N, van Vugt, R, Huang, WM, Stevenson, B, Rosa, P, Lathigra, R, Sutton, G, Peterson, J, Dodson, RJ. A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochaete Borrelia burgdorferi. Mol. Microbiol.. 2000; 35: 490-516 [OpenAIRE] [PubMed]

Canchaya, C, Proux, C, Fournous, G, Bruttin, A, Brüssow, H. Prophage genomics. Microbiol. Mol. Biol. Rev.. 2003; 67: 238-276 [OpenAIRE] [PubMed]

Mc Grath, S, Van, SD. Bacteriophage: Genetics and Molecular Biology. 2007

Aziz, RK, Ismail, S, Park, HW, Kotb, M. Post-proteomic identification of a novel phage-encoded streptodornase, Sda1, in invasive M1T1 Streptococcus pyogenes. Mol. Microbiol.. 2004; 54: 184-197 [PubMed]

Aziz, RK, Edwards, R, Taylor, WW, Low, DE, McGeer, A, Kotb, M. Mosaic prophages with horizontally acquired genes account for the emergence and diversification of the globally disseminated M1T1 clone of Streptococcus pyogenes. J. Bacteriol.. 2005; 187: 3311-3318 [OpenAIRE] [PubMed]

Campbell, A. Episomes. Adv. Genet.. 1962; 11: 101-145

Landy, A, Ross, W. Viral integration and excision: structure of the lambda att sites. Science. 1977; 197: 1147-1160 [OpenAIRE] [PubMed]

Shimada, K, Weisberg, R, Gottesman, M. Prophage lambda at unusual chromosomal locations. I. Location of the secondary attachment sites and the properties of the lysogens. J. Mol. Biol.. 1972; 63: 483-503 [OpenAIRE] [PubMed]

Rausch, H, Lehmann, M. Structural analysis of the actinophage phi C31 attachment site. Nucleic Acids Res.. 1991; 19: 5187-5189 [OpenAIRE] [PubMed]

Campbell, A, Schneider, S, Song, B. Lambdoid phages as elements of bacterial genomes (integrase/phage21/Escherichia coli K-12/icd gene). Genetica. 1992; 86: 259-267 [PubMed]

Fouts, D. Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res.. 2006; 34: 5839-5851 [OpenAIRE] [PubMed]

Altschul, SF, Gish, W, Miller, W, Myers, EW, Lipman, DJ. Basic local alignment search tool. J. Mol. Biol.. 1990; 215: 403-410 [OpenAIRE] [PubMed]

Leplae, R, Lima-Mendez, G, Toussaint, A. ACLAME: a classification of mobile genetic elements. Nucleic Acids Res.. 2004; 32: D45-D49 [OpenAIRE] [PubMed]

Lima-Mendez, G, Van, HJ, Toussaint, A, Leplae, R. Prophinder: a computational tool for prophage prediction in prokaryotic genomes. Bioinformatics. 2008; 24: 863-865 [PubMed]

55 references, page 1 of 4
Abstract
Prophages are phages in lysogeny that are integrated into, and replicated as part of, the host bacterial genome. These mobile elements can have tremendous impact on their bacterial hosts’ genomes and phenotypes, which may lead to strain emergence and diversification, increased virulence or antibiotic resistance. However, finding prophages in microbial genomes remains a problem with no definitive solution. The majority of existing tools rely on detecting genomic regions enriched in protein-coding genes with known phage homologs, which hinders the de novo discovery of phage regions. In this study, a weighted phage detection algorithm, PhiSpy was developed based on...
Subjects
Medical Subject Headings: viruses
free text keywords: Methods Online, Genetics, Prophage, Biology, GC skew, Bacterial genome size, Genome, Gene, Temperateness, Mobile genetic elements, Lysogenic cycle, Algorithm
Funded by
NSF| Collaborative Research: PHANTOME: PHage ANnotation TOols and MEthods
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0850356
  • Funding stream: Directorate for Biological Sciences | Division of Biological Infrastructure
55 references, page 1 of 4

Casjens, S. Prophages and bacterial genomics: what have we learned so far?. Mol. Microbiol.. 2003; 49: 277-300 [OpenAIRE] [PubMed]

Casjens, S, Palmer, N, van Vugt, R, Huang, WM, Stevenson, B, Rosa, P, Lathigra, R, Sutton, G, Peterson, J, Dodson, RJ. A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochaete Borrelia burgdorferi. Mol. Microbiol.. 2000; 35: 490-516 [OpenAIRE] [PubMed]

Canchaya, C, Proux, C, Fournous, G, Bruttin, A, Brüssow, H. Prophage genomics. Microbiol. Mol. Biol. Rev.. 2003; 67: 238-276 [OpenAIRE] [PubMed]

Mc Grath, S, Van, SD. Bacteriophage: Genetics and Molecular Biology. 2007

Aziz, RK, Ismail, S, Park, HW, Kotb, M. Post-proteomic identification of a novel phage-encoded streptodornase, Sda1, in invasive M1T1 Streptococcus pyogenes. Mol. Microbiol.. 2004; 54: 184-197 [PubMed]

Aziz, RK, Edwards, R, Taylor, WW, Low, DE, McGeer, A, Kotb, M. Mosaic prophages with horizontally acquired genes account for the emergence and diversification of the globally disseminated M1T1 clone of Streptococcus pyogenes. J. Bacteriol.. 2005; 187: 3311-3318 [OpenAIRE] [PubMed]

Campbell, A. Episomes. Adv. Genet.. 1962; 11: 101-145

Landy, A, Ross, W. Viral integration and excision: structure of the lambda att sites. Science. 1977; 197: 1147-1160 [OpenAIRE] [PubMed]

Shimada, K, Weisberg, R, Gottesman, M. Prophage lambda at unusual chromosomal locations. I. Location of the secondary attachment sites and the properties of the lysogens. J. Mol. Biol.. 1972; 63: 483-503 [OpenAIRE] [PubMed]

Rausch, H, Lehmann, M. Structural analysis of the actinophage phi C31 attachment site. Nucleic Acids Res.. 1991; 19: 5187-5189 [OpenAIRE] [PubMed]

Campbell, A, Schneider, S, Song, B. Lambdoid phages as elements of bacterial genomes (integrase/phage21/Escherichia coli K-12/icd gene). Genetica. 1992; 86: 259-267 [PubMed]

Fouts, D. Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res.. 2006; 34: 5839-5851 [OpenAIRE] [PubMed]

Altschul, SF, Gish, W, Miller, W, Myers, EW, Lipman, DJ. Basic local alignment search tool. J. Mol. Biol.. 1990; 215: 403-410 [OpenAIRE] [PubMed]

Leplae, R, Lima-Mendez, G, Toussaint, A. ACLAME: a classification of mobile genetic elements. Nucleic Acids Res.. 2004; 32: D45-D49 [OpenAIRE] [PubMed]

Lima-Mendez, G, Van, HJ, Toussaint, A, Leplae, R. Prophinder: a computational tool for prophage prediction in prokaryotic genomes. Bioinformatics. 2008; 24: 863-865 [PubMed]

55 references, page 1 of 4
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