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Volumn 2014, Issue , 2014, Pages

PhylOPDb: A 16S rRNA oligonucleotide probe database for prokaryotic identification

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

EID: 84908089630     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bau036     Document Type: Article
Times cited : (15)

References (37)
  • 1
    • 0028946084 scopus 로고
    • Phylogenetic identification and in situ detection of individual microbial cells without cultivation
    • Amann, R.I., Ludwig, W. and Schleifer, K.H. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev., 59, 143-169.
    • (1995) Microbiol. Rev. , vol.59 , pp. 143-169
    • Amann, R.I.1    Ludwig, W.2    Schleifer, K.H.3
  • 2
    • 3242731518 scopus 로고    scopus 로고
    • Methods of studying soil microbial diversity
    • Kirk, J.L., Beaudette, L.A., Hart, M. et al. (2004) Methods of studying soil microbial diversity. J. Microbiol. Methods, 58, 169-188.
    • (2004) J. Microbiol. Methods , vol.58 , pp. 169-188
    • Kirk, J.L.1    Beaudette, L.A.2    Hart, M.3
  • 3
    • 84879174400 scopus 로고    scopus 로고
    • Gene capture coupled to high-throughput sequencing as a strategy for targeted metagenome exploration
    • Denonfoux, J., Parisot, N., Dugat-Bony, E. et al. (2013) Gene capture coupled to high-throughput sequencing as a strategy for targeted metagenome exploration. DNA Res., 20, 185-196.
    • (2013) DNA Res. , vol.20 , pp. 185-196
    • Denonfoux, J.1    Parisot, N.2    Dugat-Bony, E.3
  • 4
    • 33746061683 scopus 로고    scopus 로고
    • Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
    • DeSantis, T.Z., Hugenholtz, P., Larsen, N. et al. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol., 72, 5069-5072.
    • (2006) Appl. Environ. Microbiol. , vol.72 , pp. 5069-5072
    • DeSantis, T.Z.1    Hugenholtz, P.2    Larsen, N.3
  • 5
    • 84873739311 scopus 로고    scopus 로고
    • The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools
    • Quast, C., Pruesse, E., Yilmaz, P. et al. (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res., 41, D590-D596.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D590-D596
    • Quast, C.1    Pruesse, E.2    Yilmaz, P.3
  • 6
    • 58149200948 scopus 로고    scopus 로고
    • The ribosomal database project: Improved alignments and new tools for rRNA analysis
    • Cole, J.R., Wang, Q., Cardenas, E. et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res., 37, D141-D145.
    • (2009) Nucleic Acids Res. , vol.37 , pp. D141-D145
    • Cole, J.R.1    Wang, Q.2    Cardenas, E.3
  • 7
    • 0036682224 scopus 로고    scopus 로고
    • PRIMROSE: A computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database
    • Ashelford, K.E., Weightman, A.J. and Fry, J.C. (2002) PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database. Nucleic Acids Res., 30, 3481-3489.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3481-3489
    • Ashelford, K.E.1    Weightman, A.J.2    Fry, J.C.3
  • 8
    • 2542523843 scopus 로고    scopus 로고
    • ARB: A software environment for sequence data
    • Ludwig, W., Strunk, O., Westram, R. et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res., 32, 1363-1371.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1363-1371
    • Ludwig, W.1    Strunk, O.2    Westram, R.3
  • 9
    • 77249087837 scopus 로고    scopus 로고
    • ORMA: A tool for identification of species-specific variations in 16S rRNA gene and oligonucleotides design
    • Severgnini, M., Cremonesi, P., Consolandi, C. et al. (2009) ORMA: a tool for identification of species-specific variations in 16S rRNA gene and oligonucleotides design. Nucleic Acids Res., 37, e109.
    • (2009) Nucleic Acids Res. , vol.37 , pp. e109
    • Severgnini, M.1    Cremonesi, P.2    Consolandi, C.3
  • 10
    • 79957828767 scopus 로고    scopus 로고
    • Comprehensive and relaxed search for oligonucleotide signatures in hierarchically clustered sequence datasets
    • Bader, K.C., Grothoff, C. and Meier, H. (2011) Comprehensive and relaxed search for oligonucleotide signatures in hierarchically clustered sequence datasets. Bioinformatics, 27, 1546-1554.
    • (2011) Bioinformatics , vol.27 , pp. 1546-1554
    • Bader, K.C.1    Grothoff, C.2    Meier, H.3
  • 11
    • 84987602902 scopus 로고    scopus 로고
    • Efficient relaxed search in hierarchically clustered sequence datasets
    • Bader, K.C., Atallah, M.J. and Grothoff, C. (2012) Efficient relaxed search in hierarchically clustered sequence datasets. J. Exp. Algorithmics (JEA), 17, 1.4.
    • (2012) J. Exp. Algorithmics (JEA) , vol.17 , pp. 14
    • Bader, K.C.1    Atallah, M.J.2    Grothoff, C.3
  • 12
    • 83655202427 scopus 로고    scopus 로고
    • Detecting unknown sequences with DNA microarrays: Explorative probe design strategies
    • Dugat-Bony, E., Peyretaillade, E., Parisot, N. et al. (2012) Detecting unknown sequences with DNA microarrays: explorative probe design strategies. Environ. Microbiol., 14, 356-371.
    • (2012) Environ. Microbiol. , vol.14 , pp. 356-371
    • Dugat-Bony, E.1    Peyretaillade, E.2    Parisot, N.3
  • 13
    • 35748938228 scopus 로고    scopus 로고
    • PhylArray: Phylogenetic probe design algorithm for microarray
    • Militon, C., Rimour, S., Missaoui, M. et al. (2007) PhylArray: phylogenetic probe design algorithm for microarray. Bioinformatics, 23, 2550-2557.
    • (2007) Bioinformatics , vol.23 , pp. 2550-2557
    • Militon, C.1    Rimour, S.2    Missaoui, M.3
  • 15
    • 84870423100 scopus 로고    scopus 로고
    • KASpOD - A web service for highly specific and explorative oligonucleotide design
    • Parisot, N., Denonfoux, J., Dugat-Bony, E. et al. (2012) KASpOD - a web service for highly specific and explorative oligonucleotide design. Bioinformatics, 28, 3161-3162.
    • (2012) Bioinformatics , vol.28 , pp. 3161-3162
    • Parisot, N.1    Denonfoux, J.2    Dugat-Bony, E.3
  • 18
    • 33846102841 scopus 로고    scopus 로고
    • ProbeBase - An online resource for rRNA-targeted oligonucleotide probes: New features 2007
    • Loy, A., Maixner, F., Wagner, M. et al. (2007) probeBase-an online resource for rRNA-targeted oligonucleotide probes: new features 2007. Nucleic Acids Res., 35, D800-D804.
    • (2007) Nucleic Acids Res. , vol.35 , pp. D800-D804
    • Loy, A.1    Maixner, F.2    Wagner, M.3
  • 19
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • Altschul, S.F., Gish, W., Miller, W. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
    • (1990) J. Mol. Biol. , vol.215 , pp. 403-410
    • Altschul, S.F.1    Gish, W.2    Miller, W.3
  • 20
    • 84984933234 scopus 로고    scopus 로고
    • High density synthetic oligonucleotide arrays
    • Lipshutz, R.J., Fodor, S.P., Gingeras, T.R. et al. (1999) High density synthetic oligonucleotide arrays. Nat. Genet., 21, 20-24.
    • (1999) Nat. Genet. , vol.21 , pp. 20-24
    • Lipshutz, R.J.1    Fodor, S.P.2    Gingeras, T.R.3
  • 21
    • 0036795787 scopus 로고    scopus 로고
    • Oligonucleotide micro-array for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment
    • Loy, A., Lehner, A., Lee, N. et al. (2002) Oligonucleotide micro-array for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl. Environ. Microbiol., 68, 5064-5081.
    • (2002) Appl. Environ. Microbiol. , vol.68 , pp. 5064-5081
    • Loy, A.1    Lehner, A.2    Lee, N.3
  • 22
    • 84857122937 scopus 로고    scopus 로고
    • An improved greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
    • McDonald, D., Price, M.N., Goodrich, J.K. et al. (2012) An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J., 6, 610-618.
    • (2012) ISME J. , vol.6 , pp. 610-618
    • McDonald, D.1    Price, M.N.2    Goodrich, J.K.3
  • 23
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li, W. and Godzik, A. (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 24
    • 0036245011 scopus 로고    scopus 로고
    • High-density microarray of small-subunit ribosomal DNA probes
    • Wilson, K.H., Wilson, W.J., Radosevich, J.L. et al. (2002) High-density microarray of small-subunit ribosomal DNA probes. Appl. Environ. Microbiol., 68, 2535-2541.
    • (2002) Appl. Environ. Microbiol. , vol.68 , pp. 2535-2541
    • Wilson, K.H.1    Wilson, W.J.2    Radosevich, J.L.3
  • 25
    • 33748805463 scopus 로고    scopus 로고
    • Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation
    • Brodie, E.L., DeSantis, T.Z., Joyner, D.C. et al. (2006) Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl. Environ. Microbiol., 72, 6288-6298.
    • (2006) Appl. Environ. Microbiol. , vol.72 , pp. 6288-6298
    • Brodie, E.L.1    DeSantis, T.Z.2    Joyner, D.C.3
  • 26
    • 31544436089 scopus 로고    scopus 로고
    • Rapid quantitative profiling of complex microbial populations
    • Palmer, C., Bik, E.M., Eisen, M.B. et al. (2006) Rapid quantitative profiling of complex microbial populations. Nucleic Acids Res., 34, e5.
    • (2006) Nucleic Acids Res. , vol.34 , pp. e5
    • Palmer, C.1    Bik, E.M.2    Eisen, M.B.3
  • 27
    • 33846035747 scopus 로고    scopus 로고
    • Urban aerosols harbor diverse and dynamic bacterial populations
    • Brodie, E.L., DeSantis, T.Z., Parker, J.P.M. et al. (2007) Urban aerosols harbor diverse and dynamic bacterial populations. Proc. Natl Acad. Sci. USA, 104, 299-304.
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 299-304
    • Brodie, E.L.1    DeSantis, T.Z.2    Parker, J.P.M.3
  • 28
    • 34248159346 scopus 로고    scopus 로고
    • High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment
    • DeSantis, T.Z., Brodie, E.L., Moberg, J.P. et al. (2007) High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb. Ecol., 53, 371-383.
    • (2007) Microb. Ecol. , vol.53 , pp. 371-383
    • DeSantis, T.Z.1    Brodie, E.L.2    Moberg, J.P.3
  • 29
    • 77956299931 scopus 로고    scopus 로고
    • Deep-sea oil plume enriches indigenous oil-degrading bacteria
    • Hazen, T.C., Dubinsky, E.A., DeSantis, T.Z. et al. (2010) Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science, 330, 204-208.
    • (2010) Science , vol.330 , pp. 204-208
    • Hazen, T.C.1    Dubinsky, E.A.2    DeSantis, T.Z.3
  • 30
    • 0033855457 scopus 로고    scopus 로고
    • Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labeled oligonucleotide probes
    • Fuchs, B.M., Glöckner, F.O., Wulf, J. et al. (2000) Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labeled oligonucleotide probes. Appl. Environ. Microbiol., 66, 3603-3607.
    • (2000) Appl. Environ. Microbiol. , vol.66 , pp. 3603-3607
    • Fuchs, B.M.1    Glöckner, F.O.2    Wulf, J.3
  • 31
    • 35748951614 scopus 로고    scopus 로고
    • Direct selection of human genomic loci by microarray hybridization
    • Albert, T.J., Molla, M.N., Muzny, D.M. et al. (2007) Direct selection of human genomic loci by microarray hybridization. Nat. Methods, 4, 903-905.
    • (2007) Nat. Methods , vol.4 , pp. 903-905
    • Albert, T.J.1    Molla, M.N.2    Muzny, D.M.3
  • 32
    • 35748959649 scopus 로고    scopus 로고
    • Microarray-based genomic selection for high-throughput rese-quencing
    • Okou, D.T., Steinberg, K.M., Middle, C. et al. (2007) Microarray-based genomic selection for high-throughput rese-quencing. Nat. Methods, 4, 907-909.
    • (2007) Nat. Methods , vol.4 , pp. 907-909
    • Okou, D.T.1    Steinberg, K.M.2    Middle, C.3
  • 33
    • 77954091424 scopus 로고    scopus 로고
    • Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries
    • Mokry, M., Feitsma, H., Nijman, I.J. et al. (2010) Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries. Nucleic Acids Res., 38, e116.
    • (2010) Nucleic Acids Res. , vol.38 , pp. e116
    • Mokry, M.1    Feitsma, H.2    Nijman, I.J.3
  • 34
    • 59849113821 scopus 로고    scopus 로고
    • Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
    • Gnirke, A., Melnikov, A., Maguire, J. et al. (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol., 27, 182-189.
    • (2009) Nat. Biotechnol. , vol.27 , pp. 182-189
    • Gnirke, A.1    Melnikov, A.2    Maguire, J.3
  • 35
    • 75349097525 scopus 로고    scopus 로고
    • Enrichment of sequencing targets from the human genome by solution hybridization
    • Tewhey, R., Nakano, M., Wang, X. et al. (2009) Enrichment of sequencing targets from the human genome by solution hybridization. Genome Biol., 10, R116.
    • (2009) Genome Biol. , vol.10 , pp. R116
    • Tewhey, R.1    Nakano, M.2    Wang, X.3
  • 36
    • 28544435896 scopus 로고    scopus 로고
    • Highly parallel microbial diagnostics using oligonucleotide microarrays
    • Loy, A. and Bodrossy, L. (2006) Highly parallel microbial diagnostics using oligonucleotide microarrays. Clin. Chim. Acta, 363, 106-119.
    • (2006) Clin. Chim. Acta , vol.363 , pp. 106-119
    • Loy, A.1    Bodrossy, L.2
  • 37
    • 77951587015 scopus 로고    scopus 로고
    • Detection of tmRNA molecules on microarrays at low temperatures using helper oligonucleotides
    • Kaplinski, L., Scheler, O., Parkel, S. et al. (2010) Detection of tmRNA molecules on microarrays at low temperatures using helper oligonucleotides. BMC Biotechnol., 10, 34.
    • (2010) BMC Biotechnol. , vol.10 , pp. 34
    • Kaplinski, L.1    Scheler, O.2    Parkel, S.3


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