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Volumn 7, Issue 11, 2012, Pages

De-MetaST-BLAST: A Tool for the Validation of Degenerate Primer Sets and Data Mining of Publicly Available Metagenomes

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER MODEL; COMPUTER PROGRAM; DATA MINING; DEGENERATE PRIMER SET; METAGENOME; NUCLEIC ACID AMPLIFICATION; NUCLEOTIDE SEQUENCE; SEQUENCE DATABASE; VALIDATION PROCESS;

EID: 84869988564     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0050362     Document Type: Article
Times cited : (13)

References (47)
  • 1
    • 1942517869 scopus 로고    scopus 로고
    • Group-specific polymerase chain reaction for DNA-based analysis of species diversity and identity in dietary samples
    • Jarman SN, Deagle BE, Gales NJ, (2004) Group-specific polymerase chain reaction for DNA-based analysis of species diversity and identity in dietary samples. Molecular Ecology 13: 1313-1322.
    • (2004) Molecular Ecology , vol.13 , pp. 1313-1322
    • Jarman, S.N.1    Deagle, B.E.2    Gales, N.J.3
  • 2
    • 23944517269 scopus 로고    scopus 로고
    • Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series
    • Brown MV, Schwalbach MS, Hewson I, Fuhrman JA, (2005) Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series. Environmental Microbiology 7: 1466-1479.
    • (2005) Environmental Microbiology , vol.7 , pp. 1466-1479
    • Brown, M.V.1    Schwalbach, M.S.2    Hewson, I.3    Fuhrman, J.A.4
  • 3
    • 69949104495 scopus 로고    scopus 로고
    • Metagenomics reveals diversity and abundance of meta-cleavage pathways in microbial communities from soil highly contaminated with jet fuel under air-sparging bioremediation
    • Brennerova MV, Josefiova J, Brenner V, Pieper DH, Junca H, (2009) Metagenomics reveals diversity and abundance of meta-cleavage pathways in microbial communities from soil highly contaminated with jet fuel under air-sparging bioremediation. Environmental Microbiology 11: 2216-2227.
    • (2009) Environmental Microbiology , vol.11 , pp. 2216-2227
    • Brennerova, M.V.1    Josefiova, J.2    Brenner, V.3    Pieper, D.H.4    Junca, H.5
  • 4
    • 47249125310 scopus 로고    scopus 로고
    • Estimation of the density of the protocatechuate-degrading bacterial community in soil by real-time PCR
    • El Azhari N, Bru D, Sarr A, Martin-Laurent F, (2008) Estimation of the density of the protocatechuate-degrading bacterial community in soil by real-time PCR. European Journal of Soil Science 59: 665-673.
    • (2008) European Journal of Soil Science , vol.59 , pp. 665-673
    • El Azhari, N.1    Bru, D.2    Sarr, A.3    Martin-Laurent, F.4
  • 5
    • 33846120159 scopus 로고    scopus 로고
    • Desulfurization of aromatic sulfonates by rhizosphere bacteria: high diversity of the asfA gene
    • Schmalenberger A, Kertesz MA, (2007) Desulfurization of aromatic sulfonates by rhizosphere bacteria: high diversity of the asfA gene. Environmental Microbiology 9: 535-545.
    • (2007) Environmental Microbiology , vol.9 , pp. 535-545
    • Schmalenberger, A.1    Kertesz, M.A.2
  • 6
    • 0346195660 scopus 로고    scopus 로고
    • Phylogenetic diversity of nitrogenase (nifH) genes in deep-sea and hydrothermal vent environments of the Juan de Fuca ridge
    • Mehta MP, Butterfield DA, Baross JA, (2003) Phylogenetic diversity of nitrogenase (nifH) genes in deep-sea and hydrothermal vent environments of the Juan de Fuca ridge. Applied and Environmental Microbiology 69: 960-970.
    • (2003) Applied and Environmental Microbiology , vol.69 , pp. 960-970
    • Mehta, M.P.1    Butterfield, D.A.2    Baross, J.A.3
  • 8
    • 0036856362 scopus 로고    scopus 로고
    • The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill
    • Luton PE, Wayne JM, Sharp RJ, Riley PW, (2002) The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology 148: 3521-3530.
    • (2002) Microbiology , vol.148 , pp. 3521-3530
    • Luton, P.E.1    Wayne, J.M.2    Sharp, R.J.3    Riley, P.W.4
  • 9
    • 33748317824 scopus 로고    scopus 로고
    • Analysis of mercuric reductase (merA) gene diversity in an anaerobic mercury-contaminated sediment enrichment
    • Chadhain SMN, Schaefer JK, Crane S, Zylstra GJ, Barkay T, (2006) Analysis of mercuric reductase (merA) gene diversity in an anaerobic mercury-contaminated sediment enrichment. Environmental Microbiology 8: 1746-1752.
    • (2006) Environmental Microbiology , vol.8 , pp. 1746-1752
    • Chadhain, S.M.N.1    Schaefer, J.K.2    Crane, S.3    Zylstra, G.J.4    Barkay, T.5
  • 11
    • 77953557020 scopus 로고    scopus 로고
    • Gene diversity of CYP153A and AlkB alkane hydroxylases in oil-degrading bacteria isolated from the Atlantic Ocean
    • Wang LP, Wang WP, Lai QL, Shao ZZ, (2010) Gene diversity of CYP153A and AlkB alkane hydroxylases in oil-degrading bacteria isolated from the Atlantic Ocean. Environmental Microbiology 12: 1230-1242.
    • (2010) Environmental Microbiology , vol.12 , pp. 1230-1242
    • Wang, L.P.1    Wang, W.P.2    Lai, Q.L.3    Shao, Z.Z.4
  • 13
    • 3543104816 scopus 로고    scopus 로고
    • Amplicon: software for designing PCR primers on aligned DNA sequences
    • Jarman SN, (2004) Amplicon: software for designing PCR primers on aligned DNA sequences. Bioinformatics 20: 1644-1645.
    • (2004) Bioinformatics , vol.20 , pp. 1644-1645
    • Jarman, S.N.1
  • 15
    • 0043122986 scopus 로고    scopus 로고
    • CODEHOP (COnsensus-DEgenerate hybrid oligonucleotide primer) PCR primer design
    • Rose TM, Henikoff JG, Henikoff S, (2003) CODEHOP (COnsensus-DEgenerate hybrid oligonucleotide primer) PCR primer design. Nucleic Acids Research 31: 3763-3766.
    • (2003) Nucleic Acids Research , vol.31 , pp. 3763-3766
    • Rose, T.M.1    Henikoff, J.G.2    Henikoff, S.3
  • 16
    • 0032052770 scopus 로고    scopus 로고
    • Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences
    • Rose TM, Schultz ER, Henikoff JG, Pietrokovski S, McCallum CM, et al. (1998) Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences. Nucleic Acids Research 26: 1628-1635.
    • (1998) Nucleic Acids Research , vol.26 , pp. 1628-1635
    • Rose, T.M.1    Schultz, E.R.2    Henikoff, J.G.3    Pietrokovski, S.4    McCallum, C.M.5
  • 17
    • 0036729225 scopus 로고    scopus 로고
    • DEFOG: A practical scheme for deciphering families of genes
    • Fuchs T, Malecova B, Linhart C, Sharan R, Khen M, et al. (2002) DEFOG: A practical scheme for deciphering families of genes. Genomics 80: 295-302.
    • (2002) Genomics , vol.80 , pp. 295-302
    • Fuchs, T.1    Malecova, B.2    Linhart, C.3    Sharan, R.4    Khen, M.5
  • 19
    • 36048970300 scopus 로고    scopus 로고
    • Degenerate primer design: theoretical analysis and the HYDEN program
    • Linhart C, Shamir R, (2007) Degenerate primer design: theoretical analysis and the HYDEN program. Methods in molecular biology (Clifton, NJ) 402: 221-244.
    • (2007) Methods in Molecular Biology (Clifton, NJ) , vol.402 , pp. 221-244
    • Linhart, C.1    Shamir, R.2
  • 20
    • 43149106710 scopus 로고    scopus 로고
    • MAD-DPD: designing highly degenerate primers with maximum amplification specificity
    • Najafabadi HS, Saberj A, Torabi N, Chamankhah M (2008) MAD-DPD: designing highly degenerate primers with maximum amplification specificity. Biotechniques 44: 519-+.
    • (2008) Biotechniques , vol.44 , pp. 519
    • Najafabadi, H.S.1    Saberj, A.2    Torabi, N.3    Chamankhah, M.4
  • 21
    • 84857680457 scopus 로고    scopus 로고
    • PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity
    • Dwivedi B, Schmieder R, Goldsmith DB, Edwards RA, Breitbart M (2012) PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity. BMC Bioinformatics 13.
    • (2012) BMC Bioinformatics , vol.13
    • Dwivedi, B.1    Schmieder, R.2    Goldsmith, D.B.3    Edwards, R.A.4    Breitbart, M.5
  • 22
    • 16344379864 scopus 로고    scopus 로고
    • Primaclade - a flexible tool to find conserved PCR primers across multiple species
    • Gadberry MD, Malcomber ST, Doust AN, Kellogg EA, (2005) Primaclade- a flexible tool to find conserved PCR primers across multiple species. Bioinformatics 21: 1263-1264.
    • (2005) Bioinformatics , vol.21 , pp. 1263-1264
    • Gadberry, M.D.1    Malcomber, S.T.2    Doust, A.N.3    Kellogg, E.A.4
  • 25
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28: 2731-2739.
    • (2011) Molecular Biology and Evolution , vol.28 , pp. 2731-2739
    • Tamura, K.1    Peterson, D.2    Peterson, N.3    Stecher, G.4    Nei, M.5
  • 26
    • 0028117341 scopus 로고
    • A guide to the design and use of mismatched and degenerate primers
    • Kwok S, Chang SY, Sninsky JJ, Wang A, (1994) A guide to the design and use of mismatched and degenerate primers. Genome Research 3: S39-S47.
    • (1994) Genome Research , vol.3
    • Kwok, S.1    Chang, S.Y.2    Sninsky, J.J.3    Wang, A.4
  • 27
    • 1142281826 scopus 로고    scopus 로고
    • Functional gene diversity analysis in BTEX contaminated soils by means of PCR-SSCP DNA fingerprinting: comparative diversity assessment against bacterial isolates and PCR-DNA clone libraries
    • Junca H, Pieper DH, (2004) Functional gene diversity analysis in BTEX contaminated soils by means of PCR-SSCP DNA fingerprinting: comparative diversity assessment against bacterial isolates and PCR-DNA clone libraries. Environmental Microbiology 6: 95-110.
    • (2004) Environmental Microbiology , vol.6 , pp. 95-110
    • Junca, H.1    Pieper, D.H.2
  • 28
    • 30944440673 scopus 로고    scopus 로고
    • Alternative primer sets for PCR detection of genotypes involved in bacterial aerobic BTEX degradation: Distribution of the genes in BTEX degrading isolates and in subsurface soils of a BTEX contaminated industrial site
    • Hendrickx B, Junca H, Vosahlova J, Lindner A, Ruegg I, et al. (2006) Alternative primer sets for PCR detection of genotypes involved in bacterial aerobic BTEX degradation: Distribution of the genes in BTEX degrading isolates and in subsurface soils of a BTEX contaminated industrial site. Journal of Microbiological Methods 64: 250-265.
    • (2006) Journal of Microbiological Methods , vol.64 , pp. 250-265
    • Hendrickx, B.1    Junca, H.2    Vosahlova, J.3    Lindner, A.4    Ruegg, I.5
  • 29
    • 0042208392 scopus 로고    scopus 로고
    • Diversity of ascomycete laccase gene sequences in a southeastern US salt marsh
    • Lyons JI, Newell SY, Buchan A, Moran MA, (2003) Diversity of ascomycete laccase gene sequences in a southeastern US salt marsh. Microbial Ecology 45: 270-281.
    • (2003) Microbial Ecology , vol.45 , pp. 270-281
    • Lyons, J.I.1    Newell, S.Y.2    Buchan, A.3    Moran, M.A.4
  • 30
    • 13944267988 scopus 로고    scopus 로고
    • Characterization of diatom (Bacillariophyceae) nitrate reductase genes and their detection in marine phytoplankton communities
    • Allen AE, Ward BB, Song BK, (2005) Characterization of diatom (Bacillariophyceae) nitrate reductase genes and their detection in marine phytoplankton communities. Journal of Phycology 41: 95-104.
    • (2005) Journal of Phycology , vol.41 , pp. 95-104
    • Allen, A.E.1    Ward, B.B.2    Song, B.K.3
  • 31
    • 77957000882 scopus 로고    scopus 로고
    • Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans
    • Malmstrom RR, Coe A, Kettler GC, Martiny AC, Frias-Lopez J, et al. (2010) Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans. ISME Journal 4: 1252-1264.
    • (2010) ISME Journal , vol.4 , pp. 1252-1264
    • Malmstrom, R.R.1    Coe, A.2    Kettler, G.C.3    Martiny, A.C.4    Frias-Lopez, J.5
  • 32
    • 34547567980 scopus 로고    scopus 로고
    • OligoCalc: an online oligonucleotide properties calculator
    • Kibbe WA, (2007) OligoCalc: an online oligonucleotide properties calculator. Nucleic Acids Research 35: W43-W46.
    • (2007) Nucleic Acids Research , vol.35
    • Kibbe, W.A.1
  • 33
    • 0242573334 scopus 로고    scopus 로고
    • Diversity and abundance of uncultured Cytophaga-like bacteria in the Delaware Estuary
    • Kirchman DL, Yu LY, Cottrell MT, (2003) Diversity and abundance of uncultured Cytophaga-like bacteria in the Delaware Estuary. Applied and Environmental Microbiology 69: 6587-6596.
    • (2003) Applied and Environmental Microbiology , vol.69 , pp. 6587-6596
    • Kirchman, D.L.1    Yu, L.Y.2    Cottrell, M.T.3
  • 36
    • 0030814870 scopus 로고    scopus 로고
    • The ammonia monooxygenase structural gene amoA as a functional marker: Molecular fine-scale analysis of natural ammonia-oxidizing populations
    • Rotthauwe JH, Witzel KP, Liesack W, (1997) The ammonia monooxygenase structural gene amoA as a functional marker: Molecular fine-scale analysis of natural ammonia-oxidizing populations. Applied and Environmental Microbiology 63: 4704-4712.
    • (1997) Applied and Environmental Microbiology , vol.63 , pp. 4704-4712
    • Rotthauwe, J.H.1    Witzel, K.P.2    Liesack, W.3
  • 38
    • 78651266825 scopus 로고    scopus 로고
    • Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource
    • Sun S, Chen J, Li W, Altintas I, Lin A, et al. (2011) Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Research 39: D546-D551.
    • (2011) Nucleic Acids Research , vol.39
    • Sun, S.1    Chen, J.2    Li, W.3    Altintas, I.4    Lin, A.5
  • 40
    • 77954224688 scopus 로고    scopus 로고
    • Coenzyme A-dependent aerobic metabolism of benzoate via epoxide formation
    • Rather LJ, Knapp B, Haehnel W, Fuchs G, (2010) Coenzyme A-dependent aerobic metabolism of benzoate via epoxide formation. Journal of Biological Chemistry 285: 20615-20624.
    • (2010) Journal of Biological Chemistry , vol.285 , pp. 20615-20624
    • Rather, L.J.1    Knapp, B.2    Haehnel, W.3    Fuchs, G.4
  • 42
    • 79958257334 scopus 로고    scopus 로고
    • Comparison of the specificities and efficacies of primers for aromatic dioxygenase gene analysis of environmental samples
    • Iwai S, Johnson TA, Chai B, Hashsham SA, Tiedje JM, (2011) Comparison of the specificities and efficacies of primers for aromatic dioxygenase gene analysis of environmental samples. Applied and Environmental Microbiology 77: 3551-3557.
    • (2011) Applied and Environmental Microbiology , vol.77 , pp. 3551-3557
    • Iwai, S.1    Johnson, T.A.2    Chai, B.3    Hashsham, S.A.4    Tiedje, J.M.5
  • 44
    • 0030635789 scopus 로고    scopus 로고
    • Cloning gene family members using the polymerase chain reaction with degenerate oligonucleotide primers
    • Preston GM, (1997) Cloning gene family members using the polymerase chain reaction with degenerate oligonucleotide primers. Methods in Molecular Biology (Clifton, N.J.) 69: 97-113.
    • (1997) Methods in Molecular Biology (Clifton, N.J.) , vol.69 , pp. 97-113
    • Preston, G.M.1
  • 45
    • 0028123422 scopus 로고
    • PCR amplification using deoxyinosine to replace entire codon and at ambiguous positions
    • Liu H, Nichols R, (1994) PCR amplification using deoxyinosine to replace entire codon and at ambiguous positions. Biotechniques 16: 24-26.
    • (1994) Biotechniques , vol.16 , pp. 24-26
    • Liu, H.1    Nichols, R.2
  • 46
    • 72949107142 scopus 로고    scopus 로고
    • Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
    • Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 75: 7537-7541.
    • (2009) Applied and Environmental Microbiology , vol.75 , pp. 7537-7541
    • Schloss, P.D.1    Westcott, S.L.2    Ryabin, T.3    Hall, J.R.4    Hartmann, M.5
  • 47
    • 0027460328 scopus 로고
    • Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
    • Muyzer G, Dewaal EC, Uitterlinden AG, (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology 59: 695-700.
    • (1993) Applied and Environmental Microbiology , vol.59 , pp. 695-700
    • Muyzer, G.1    Dewaal, E.C.2    Uitterlinden, A.G.3


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