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Volumn 25, Issue 11, 2009, Pages 1349-1355

Automatic identification of species-specific repetitive DNA sequences and their utilization for detecting microbial organisms

Author keywords

[No Author keywords available]

Indexed keywords

PRIMER DNA; REPETITIVE DNA;

EID: 65649098025     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp241     Document Type: Article
Times cited : (17)

References (37)
  • 1
    • 0035211889 scopus 로고    scopus 로고
    • Study of intrachromosomal duplications among the eukaryote genomes
    • Achaz,G. et al. (2001) Study of intrachromosomal duplications among the eukaryote genomes. Mol. Biol. Evol., 18, 2280-2288.
    • (2001) Mol. Biol. Evol , vol.18 , pp. 2280-2288
    • Achaz, G.1
  • 2
    • 0036640350 scopus 로고    scopus 로고
    • Origin and fate of repeats in bacteria
    • Achaz,G. et al. (2002) Origin and fate of repeats in bacteria. Nucleic Acids Res., 30, 2987-2994.
    • (2002) Nucleic Acids Res , vol.30 , pp. 2987-2994
    • Achaz, G.1
  • 3
    • 0042318548 scopus 로고    scopus 로고
    • Association between inverted repeats and the structural evolution of bacterial genomes
    • Achaz,G. et al. (2003) Association between inverted repeats and the structural evolution of bacterial genomes. Genetics, 164 1279-1289.
    • (2003) Genetics , vol.164 , pp. 1279-1289
    • Achaz, G.1
  • 4
    • 46349105615 scopus 로고    scopus 로고
    • Predicting failure rate of PCR in large genomes
    • Andreson,R. et al. (2008) Predicting failure rate of PCR in large genomes. Nucleic Acids Res., 36, e66.
    • (2008) Nucleic Acids Res , vol.36
    • Andreson, R.1
  • 5
    • 1642326634 scopus 로고    scopus 로고
    • Fungal molecular diagnostics: A mini review
    • Atkins,S.D. and Clark,I.M. (2004) Fungal molecular diagnostics: A mini review. J. Appl. Genet., 45, 3-15.
    • (2004) J. Appl. Genet , vol.45 , pp. 3-15
    • Atkins, S.D.1    Clark, I.M.2
  • 6
    • 0242384034 scopus 로고    scopus 로고
    • Review and re-analysis of domain specific 16S primers
    • Baker,G.C. et al. (2003) Review and re-analysis of domain specific 16S primers. J. Microbiol. Methods, 55, 541-555.
    • (2003) J. Microbiol. Methods , vol.55 , pp. 541-555
    • Baker, G.C.1
  • 7
    • 33646478851 scopus 로고    scopus 로고
    • Molecular genetic anatomy of inter- and intraserotype variation in the human bacterial pathogen groupAStreptococcus
    • Beres,S.B. et al. (2006) Molecular genetic anatomy of inter- and intraserotype variation in the human bacterial pathogen groupAStreptococcus. Proc. Natl Acad. Sci. USA, 103, 7059-7064.
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 7059-7064
    • Beres, S.B.1
  • 8
    • 18544378317 scopus 로고    scopus 로고
    • Evaluation of conventional and real-time PCR assays using two targets for confirmation of the COBAS AMPLICOR CT/ NG test for Neisseria gonorrhoeae in clinical samples
    • Boel,C.H.E. et al. (2005) Evaluation of conventional and real-time PCR assays using two targets for confirmation of the COBAS AMPLICOR CT/ NG test for Neisseria gonorrhoeae in clinical samples. J. Clin. Microbiol., 43, 2231-2235.
    • (2005) J. Clin. Microbiol , vol.43 , pp. 2231-2235
    • Boel, C.H.E.1
  • 9
    • 2442636328 scopus 로고    scopus 로고
    • False-positive results and contamination in nucleic acid amplification assays: Suggestions for a prevent and destroy strategy
    • Borst,A. et al. (2004) False-positive results and contamination in nucleic acid amplification assays: Suggestions for a prevent and destroy strategy. Eur. J. Microbiol. Infect. Dis., 23, 289-299.
    • (2004) Eur. J. Microbiol. Infect. Dis , vol.23 , pp. 289-299
    • Borst, A.1
  • 10
    • 4644226917 scopus 로고    scopus 로고
    • Multicenter validation of the cppB gene as a PCR target for detection of Neisseria gonorrhoeae
    • Bruisten,S.M. et al. (2004) Multicenter validation of the cppB gene as a PCR target for detection of Neisseria gonorrhoeae. J. Clin. Microbiol., 42, 4332-4334.
    • (2004) J. Clin. Microbiol , vol.42 , pp. 4332-4334
    • Bruisten, S.M.1
  • 11
    • 0032907041 scopus 로고    scopus 로고
    • Evaluation of AMPLICOR Neisseria gonorrhoeae PCR using cppB nested PCR and 16S rRNA PCR
    • Farrell,D.J. (1999) Evaluation of AMPLICOR Neisseria gonorrhoeae PCR using cppB nested PCR and 16S rRNA PCR. J. Clin. Microb., 37 386-390.
    • (1999) J. Clin. Microb , vol.37 , pp. 386-390
    • Farrell, D.J.1
  • 12
    • 0347093249 scopus 로고    scopus 로고
    • Use of genome selected repeated sequences increases the sensitivity of PCR detection of Tropheryma whipplei
    • Fenollar,F. et al. (2003) Use of genome selected repeated sequences increases the sensitivity of PCR detection of Tropheryma whipplei. J. Clin. Microbiol., 42, 401-403.
    • (2003) J. Clin. Microbiol , vol.42 , pp. 401-403
    • Fenollar, F.1
  • 13
    • 0242593806 scopus 로고    scopus 로고
    • Comparision of PCR and serological assays for early diagnosis of acute Q fever
    • Fournier,P.E. and Raoult,D. (2003) Comparision of PCR and serological assays for early diagnosis of acute Q fever. J. Clin. Microbiol., 41, 5094-5098.
    • (2003) J. Clin. Microbiol , vol.41 , pp. 5094-5098
    • Fournier, P.E.1    Raoult, D.2
  • 14
    • 35548934170 scopus 로고    scopus 로고
    • Primique: Automatic design of specific PCR primers for each sequence in a family
    • Fredslund,J. and Lange,M. (2007) Primique: Automatic design of specific PCR primers for each sequence in a family. BMC Bioinformatics, 8, 369.
    • (2007) BMC Bioinformatics , vol.8 , pp. 369
    • Fredslund, J.1    Lange, M.2
  • 15
    • 23144467843 scopus 로고    scopus 로고
    • PriFi: Using a multiple alignment of related sequences to find primers for amplification of homologs
    • Fredslund,J. et al. (2005) PriFi: Using a multiple alignment of related sequences to find primers for amplification of homologs. Nucleic Acids Res., 33, W516-W520.
    • (2005) Nucleic Acids Res , vol.33
    • Fredslund, J.1
  • 16
    • 39749124204 scopus 로고    scopus 로고
    • PRISE (PRImer SElector): Software for designing sequence-selective PCR primers
    • Fu,Q. et al. (2008) PRISE (PRImer SElector): Software for designing sequence-selective PCR primers. J. Microbiol. Methods, 72, 263-267.
    • (2008) J. Microbiol. Methods , vol.72 , pp. 263-267
    • Fu, Q.1
  • 17
    • 0028044921 scopus 로고
    • PCR primers and probes for the 16S rRNA gene of most species of pathogenic bacteria, including bacteria found in cerebrospinal fluid
    • Greisen,M.L. and Purohit,A. (1994) PCR primers and probes for the 16S rRNA gene of most species of pathogenic bacteria, including bacteria found in cerebrospinal fluid. J. Clin. Microbiol., 32, 335-351.
    • (1994) J. Clin. Microbiol , vol.32 , pp. 335-351
    • Greisen, M.L.1    Purohit, A.2
  • 18
    • 33745110949 scopus 로고    scopus 로고
    • Effect of heat and pressure processing on DNA fragmentation and implications for the detection of meat using a real-time polymerase chain reaction
    • Hird,H. et al. (2006) Effect of heat and pressure processing on DNA fragmentation and implications for the detection of meat using a real-time polymerase chain reaction. Food Addit. Contam., 7, 645-650.
    • (2006) Food Addit. Contam , vol.7 , pp. 645-650
    • Hird, H.1
  • 19
    • 0023000579 scopus 로고
    • Homology of cryptic plasmid of Neisseria gonorrhoeae with plasmids from Neisseria meningitidis and Neisseria lactamica
    • Ison,C.A. et al. (1986) Homology of cryptic plasmid of Neisseria gonorrhoeae with plasmids from Neisseria meningitidis and Neisseria lactamica. J. Clin. Pathol., 39, 1119-1123
    • (1986) J. Clin. Pathol , vol.39 , pp. 1119-1123
    • Ison, C.A.1
  • 20
    • 34548738981 scopus 로고    scopus 로고
    • QPRIMER: A quick web-based application for designing conserved PCR primers from multigenome alignments
    • Kim,N. and Lee,C. (2007) QPRIMER: A quick web-based application for designing conserved PCR primers from multigenome alignments. Bioinformatics, 23, 2331-2333.
    • (2007) Bioinformatics , vol.23 , pp. 2331-2333
    • Kim, N.1    Lee, C.2
  • 21
    • 32044463133 scopus 로고    scopus 로고
    • Highly sensitive real-time PCR for specific detection and quantification of Coxiella burnetii
    • Klee,S.K. et al. (2006) Highly sensitive real-time PCR for specific detection and quantification of Coxiella burnetii. BMC Microbiol., 6, 2.
    • (2006) BMC Microbiol , vol.6 , pp. 2
    • Klee, S.K.1
  • 22
    • 34447321852 scopus 로고    scopus 로고
    • Enhancements and modifications of primer design program Primer3
    • Koressaar,T. and Remm,M. (2007) Enhancements and modifications of primer design program Primer3. Bioinformatics, 23, 1289-1291.
    • (2007) Bioinformatics , vol.23 , pp. 1289-1291
    • Koressaar, T.1    Remm, M.2
  • 23
    • 0028783493 scopus 로고
    • Single-step PCR for detection of Brucella spp. from blood and milk of infected animals
    • Leal-Klevezas,D.S. et al. (1995) Single-step PCR for detection of Brucella spp. from blood and milk of infected animals. J. Clin. Microbiol., 33, 3087-3090.
    • (1995) J. Clin. Microbiol , vol.33 , pp. 3087-3090
    • Leal-Klevezas, D.S.1
  • 24
    • 0035710746 scopus 로고    scopus 로고
    • Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCt method
    • Livak,K.J. and Schmittgen,T.D. (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCt method. Methods, 25, 402-408.
    • (2001) Methods , vol.25 , pp. 402-408
    • Livak, K.J.1    Schmittgen, T.D.2
  • 25
    • 18144441008 scopus 로고    scopus 로고
    • Innovative tools for detection of plant pathogenic viruses and bacteria
    • Lopez,M.M. et al. (2003) Innovative tools for detection of plant pathogenic viruses and bacteria. Int. Microbiol., 6, 233-243.
    • (2003) Int. Microbiol , vol.6 , pp. 233-243
    • Lopez, M.M.1
  • 26
    • 57349084131 scopus 로고    scopus 로고
    • Genome sequence of a nephritogenic and highly transformable M49 strain of streptococcus pyogenes
    • Epub ahead of print, doi:10.1128/JB.00672-08, September 26
    • McShan,W.M. et al. (2008) Genome sequence of a nephritogenic and highly transformable M49 strain of streptococcus pyogenes. J. Bacteriol. [Epub ahead of print, doi:10.1128/JB.00672-08, September 26, 2008].
    • (2008) J. Bacteriol
    • McShan, W.M.1
  • 27
    • 0037767565 scopus 로고    scopus 로고
    • Improvement in the specificity and sensitivity of detection for the Taura syndrome virus and yellow head virus of penaeid shrimp by increasing the amplicon size in SYBR Green real-time RT-PCR
    • Mouillesseaux,K.P. et al. (2003) Improvement in the specificity and sensitivity of detection for the Taura syndrome virus and yellow head virus of penaeid shrimp by increasing the amplicon size in SYBR Green real-time RT-PCR. J. Virol. Methods, 111, 121-127.
    • (2003) J. Virol. Methods , vol.111 , pp. 121-127
    • Mouillesseaux, K.P.1
  • 28
    • 53349117675 scopus 로고    scopus 로고
    • ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS)
    • Otto,T.D. et al. (2008) ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS). BMC Bioinformatics, 9, 366.
    • (2008) BMC Bioinformatics , vol.9 , pp. 366
    • Otto, T.D.1
  • 29
    • 17244381207 scopus 로고    scopus 로고
    • Normalization of soil DNA extraction for accurate quantification of target genes by real-time PCR and DGGE
    • Park,J.W. and Crowley,D.E. (2005) Normalization of soil DNA extraction for accurate quantification of target genes by real-time PCR and DGGE. BioTechniques, 38, 579-586.
    • (2005) BioTechniques , vol.38 , pp. 579-586
    • Park, J.W.1    Crowley, D.E.2
  • 30
    • 0032843459 scopus 로고    scopus 로고
    • Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in bacillus subtilis and other competent prokaryotes
    • Rocha,E.P.C. et al. (1999) Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in bacillus subtilis and other competent prokaryotes. Mol. Biol. Evol., 9, 1219-1230.
    • (1999) Mol. Biol. Evol , vol.9 , pp. 1219-1230
    • Rocha, E.P.C.1
  • 31
    • 0004222748 scopus 로고    scopus 로고
    • Available at, last accessed date 5 January, 2009
    • Rozen,S. and Skaletsky,H. (1998) Primer3. Available at http://wwwgenome.wi.mit.edu/genome_software/other/primer3.html (last accessed date 5 January, 2009)
    • (1998) Primer3
    • Rozen, S.1    Skaletsky, H.2
  • 33
    • 21144446534 scopus 로고    scopus 로고
    • The atlas visualisation of genome-wide information
    • Skovgaard,M. et al. (2002) The atlas visualisation of genome-wide information. Meth. Microbiol., 33, 49-63.
    • (2002) Meth. Microbiol , vol.33 , pp. 49-63
    • Skovgaard, M.1
  • 34
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson,J.D. et al. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1
  • 35
    • 0020575822 scopus 로고
    • DNA hybridization technique for the detection of Neisseria gonorrhoeae in men with urethritis
    • Totten,P.A. et al. (1983) DNA hybridization technique for the detection of Neisseria gonorrhoeae in men with urethritis. J. Infect. Dis., 148, 462-471.
    • (1983) J. Infect. Dis , vol.148 , pp. 462-471
    • Totten, P.A.1
  • 36
    • 9144239983 scopus 로고    scopus 로고
    • Genome update: DNA repeats in bacterial genomes
    • Ussery,D.W. et al. 2004 Genome update: DNA repeats in bacterial genomes. Microbiology, 150, 3519-3521.
    • (2004) Microbiology , vol.150 , pp. 3519-3521
    • Ussery, D.W.1
  • 37
    • 0035056342 scopus 로고    scopus 로고
    • Development of genomics-based PCR assay for detection of Mycoplasma pneumoniae in a large outbreak in New York state
    • Waring,A.L. et al. (2001) Development of genomics-based PCR assay for detection of Mycoplasma pneumoniae in a large outbreak in New York state. J. Clin. Microbiol., 39, 1385-1390.
    • (2001) J. Clin. Microbiol , vol.39 , pp. 1385-1390
    • Waring, A.L.1


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