Home LiteratureArticle Details
PMID: 22584627 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

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

Nucleic acids research ·Vol. 40 ·No. 16 ·2012-09-00 ·Pages e126

Akhter S, Aziz RK, Edwards RA

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 seven distinctive characteristics of prophages, i.e. protein length, transcription strand directionality, customized AT and GC skew, the abundance of unique phage words, phage insertion points and the similarity of phage proteins. The first five characteristics are capable of identifying prophages without any sequence similarity with known phage genes. PhiSpy locates prophages by ranking genomic regions enriched in distinctive phage traits, which leads to the successful prediction of 94% of prophages in 50 complete bacterial genomes with a 6% false-negative rate and a 0.66% false-positive rate.

MeSH Terms
Algorithms Base Composition Codon DNA, Bacterial/chemistry Genome, Bacterial Prophages/genetics Transcription, Genetic Viral Proteins/genetics
Chemicals
Codon DNA, Bacterial Viral Proteins
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Akhter Sajia
Computational Science Research Center, Department of Computer Science, San Diego State University, San Diego, CA 92182, USA. [email protected]
Aziz Ramy K
Edwards Robert A
References (47)
47 references, click to expand
  1. Contribution of exogenous genetic elements to the group A Streptococcus metagenome.
    PLoS One. 2007 Aug 29;2(8):e800 PMID: 17726530
  2. Comparative genomic analysis of 60 Mycobacteriophage genomes: genome clustering, gene acquisition, and gene size.
    J Mol Biol. 2010 Mar 19;397(1):119-43 PMID: 20064525
  3. Accessing the SEED genome databases via Web services API: tools for programmers.
    BMC Bioinformatics. 2010 Jun 14;11:319 PMID: 20546611
  4. The complete genome sequence of Mycobacterium bovis.
    Proc Natl Acad Sci U S A. 2003 Jun 24;100(13):7877-82 PMID: 12788972
  5. The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates.
    J Bacteriol. 2008 Oct;190(20):6881-93 PMID: 18676672
  6. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7.
    Nature. 2001 Jan 25;409(6819):529-33 PMID: 11206551
  7. Viral integration and excision: structure of the lambda att sites.
    Science. 1977 Sep 16;197(4309):1147-60 PMID: 331474
  8. Analyzing genomes with cumulative skew diagrams.
    Nucleic Acids Res. 1998 May 15;26(10):2286-90 PMID: 9580676
  9. Asymmetric substitution patterns in the two DNA strands of bacteria.
    Mol Biol Evol. 1996 May;13(5):660-5 PMID: 8676740
  10. Bacteriophage Mu genome sequence: analysis and comparison with Mu-like prophages in Haemophilus, Neisseria and Deinococcus.
    J Mol Biol. 2002 Mar 29;317(3):337-59 PMID: 11922669
  11. Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences.
    Nucleic Acids Res. 2006;34(20):5839-51 PMID: 17062630
  12. Comparative DNA analysis across diverse genomes.
    Annu Rev Genet. 1998;32:185-225 PMID: 9928479
  13. Structural analysis of the actinophage phi C31 attachment site.
    Nucleic Acids Res. 1991 Oct 11;19(19):5187-9 PMID: 1656389
  14. Prophages and bacterial genomics: what have we learned so far?
    Mol Microbiol. 2003 Jul;49(2):277-300 PMID: 12886937
  15. Genome sequence of Staphylococcus aureus strain Newman and comparative analysis of staphylococcal genomes: polymorphism and evolution of two major pathogenicity islands.
    J Bacteriol. 2008 Jan;190(1):300-10 PMID: 17951380
  16. Characterization of the ELPhiS prophage from Salmonella enterica serovar Enteritidis strain LK5.
    Appl Environ Microbiol. 2012 Mar;78(6):1785-93 PMID: 22247173
  17. Prophinder: a computational tool for prophage prediction in prokaryotic genomes.
    Bioinformatics. 2008 Mar 15;24(6):863-5 PMID: 18238785
  18. Lambdoid phages as elements of bacterial genomes (integrase/phage21/Escherichia coli K-12/icd gene).
    Genetica. 1992;86(1-3):259-67 PMID: 1468648
  19. Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18.
    J Bacteriol. 2003 Apr;185(7):2330-7 PMID: 12644504
  20. Skewed oligomers and origins of replication.
    Gene. 1998 Sep 14;217(1-2):57-67 PMID: 9795135
  21. Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species.
    Nucleic Acids Res. 2004 Apr 28;32(8):2386-95 PMID: 15115801
  22. Prophage genomics.
    Microbiol Mol Biol Rev. 2003 Jun;67(2):238-76, table of contents PMID: 12794192
  23. Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens.
    Genome Biol. 2009;10(5):R51 PMID: 19432983
  24. Preferential orientation of natural lambdoid prophages and bacterial chromosome organization.
    Theor Popul Biol. 2002 Jun;61(4):503-7 PMID: 12167370
  25. The genome sequence of avian pathogenic Escherichia coli strain O1:K1:H7 shares strong similarities with human extraintestinal pathogenic E. coli genomes.
    J Bacteriol. 2007 Apr;189(8):3228-36 PMID: 17293413
  26. Genome plasticity of BCG and impact on vaccine efficacy.
    Proc Natl Acad Sci U S A. 2007 Mar 27;104(13):5596-601 PMID: 17372194
  27. The complete genome sequence of Escherichia coli K-12.
    Science. 1997 Sep 5;277(5331):1453-62 PMID: 9278503
  28. The complete genome sequence of Mycobacterium avium subspecies paratuberculosis.
    Proc Natl Acad Sci U S A. 2005 Aug 30;102(35):12344-9 PMID: 16116077
  29. Properties of a general model of DNA evolution under no-strand-bias conditions.
    J Mol Evol. 1995 Mar;40(3):326-30 PMID: 7723059
  30. Identification of prophages in bacterial genomes by dinucleotide relative abundance difference.
    PLoS One. 2007 Nov 21;2(11):e1193 PMID: 18030328
  31. A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi.
    Mol Microbiol. 2000 Feb;35(3):490-516 PMID: 10672174
  32. Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain.
    J Bacteriol. 2005 Apr;187(7):2426-38 PMID: 15774886
  33. Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance.
    Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9786-91 PMID: 15213324
  34. Computational identification of operons in microbial genomes.
    Genome Res. 2002 Aug;12(8):1221-30 PMID: 12176930
  35. ACLAME: a CLAssification of Mobile genetic Elements.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D45-9 PMID: 14681355
  36. Mosaic prophages with horizontally acquired genes account for the emergence and diversification of the globally disseminated M1T1 clone of Streptococcus pyogenes.
    J Bacteriol. 2005 May;187(10):3311-8 PMID: 15866915
  37. The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice.
    Nucleic Acids Res. 2005 Jan 26;33(2):577-86 PMID: 15673718
  38. Intrastrand parity rules of DNA base composition and usage biases of synonymous codons.
    J Mol Evol. 1995 Mar;40(3):318-25 PMID: 7723058
  39. Mobile genetic elements in the genome of the beneficial rhizobacterium Pseudomonas fluorescens Pf-5.
    BMC Microbiol. 2009 Jan 13;9:8 PMID: 19144133
  40. Complete genome sequence of an M1 strain of Streptococcus pyogenes.
    Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4658-63 PMID: 11296296
  41. Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes.
    J Bacteriol. 2006 Nov;188(21):7405-15 PMID: 16936040
  42. Genome landscapes and bacteriophage codon usage.
    PLoS Comput Biol. 2008 Feb 29;4(2):e1000001 PMID: 18463708
  43. Post-proteomic identification of a novel phage-encoded streptodornase, Sda1, in invasive M1T1 Streptococcus pyogenes.
    Mol Microbiol. 2004 Oct;54(1):184-97 PMID: 15458415
  44. Prophage lambda at unusual chromosomal locations. I. Location of the secondary attachment sites and the properties of the lysogens.
    J Mol Biol. 1972 Feb 14;63(3):483-503 PMID: 4552408
  45. Basic local alignment search tool.
    J Mol Biol. 1990 Oct 5;215(3):403-10 PMID: 2231712
  46. Use of an ordered cosmid library to deduce the genomic organization of Mycobacterium leprae.
    Mol Microbiol. 1993 Jan;7(2):197-206 PMID: 8446027
  47. Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences.
    Mol Syst Biol. 2009;5:311 PMID: 19888206
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gks406
Email
[email protected]
Published
2012-09-00
Epub
2012-00-14
Pages
e126
Language
English
Region
England
NLM ID
0411011
PMCID
PMC3439882
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gks406 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2