메뉴 건너뛰기




Volumn 27, Issue 11, 2011, Pages 1546-1554

Comprehensive and relaxed search for oligonucleotide signatures in hierarchically clustered sequence datasets

Author keywords

[No Author keywords available]

Indexed keywords

PRIMER DNA;

EID: 79957828767     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr161     Document Type: Article
Times cited : (13)

References (33)
  • 1
    • 42349093774 scopus 로고    scopus 로고
    • Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques
    • Amann,R. and Fuchs,B.M. (2008) Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Nat. Rev. Microbiol., 6, 339-348.
    • (2008) Nat. Rev. Microbiol. , vol.6 , pp. 339-348
    • Amann, R.1    Fuchs, B.M.2
  • 2
    • 0025294528 scopus 로고
    • Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations
    • Amann,R.I. et al. (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol., 56, 1919-1925.
    • (1990) Appl. Environ. Microbiol. , vol.56 , pp. 1919-1925
    • Amann, R.I.1
  • 3
    • 77950919873 scopus 로고    scopus 로고
    • Development of a 16S rRNA-targeted probe set for Verrucomicrobia and its application for fluorescence in situ hybridization in a humic lake
    • Arnds,J. et al. (2010) Development of a 16S rRNA-targeted probe set for Verrucomicrobia and its application for fluorescence in situ hybridization in a humic lake. Syst. Appl. Microbiol., 33, 139-148.
    • (2010) Syst. Appl. Microbiol. , vol.33 , pp. 139-148
    • Arnds, J.1
  • 4
    • 0036682224 scopus 로고    scopus 로고
    • PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNAoligonucleotide probes and primers in conjunction with the RDP-II database
    • Ashelford,K.E. et al. (2002) PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNAoligonucleotide 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
  • 6
    • 70349886587 scopus 로고    scopus 로고
    • PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds
    • Chen,Y. et al. (2009) PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. Bioinformatics, 25, 2514-2521.
    • (2009) Bioinformatics , vol.25 , pp. 2514-2521
    • Chen, Y.1
  • 7
    • 27944465771 scopus 로고    scopus 로고
    • Design of long oligonucleotide probes for functional gene detection in a microbial community
    • Chung,W.H. et al. (2005) Design of long oligonucleotide probes for functional gene detection in a microbial community. Bioinformatics, 21, 4092-4100.
    • (2005) Bioinformatics , vol.21 , pp. 4092-4100
    • Chung, W.H.1
  • 8
    • 58149200948 scopus 로고    scopus 로고
    • The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
    • Cole,J.R. 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
    • Cole, J.R.1
  • 9
    • 33746061683 scopus 로고    scopus 로고
    • Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
    • DeSantis,T.Z. et al. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Micorbiol., 72, 5069-5072.
    • (2006) Appl. Environ. Micorbiol. , vol.72 , pp. 5069-5072
    • DeSantis, T.Z.1
  • 10
    • 34447332244 scopus 로고    scopus 로고
    • A fast and flexible approach to oligonucleotide probe design for genomes and gene families
    • Feng,S. and Tillier,E.R.M.R. (2007) A fast and flexible approach to oligonucleotide probe design for genomes and gene families. Bioinformatics, 23, 1195-1202.
    • (2007) Bioinformatics , vol.23 , pp. 1195-1202
    • Feng, S.1    Tillier, E.R.M.R.2
  • 11
    • 0036772248 scopus 로고    scopus 로고
    • Selecting signature oligonucleotides to identify organisms using DNA arrays
    • Kaderali,L. and Schliep,A. (2002) Selecting signature oligonucleotides to identify organisms using DNA arrays. Bioinformatics, 18, 1340-1349.
    • (2002) Bioinformatics , vol.18 , pp. 1340-1349
    • Kaderali, L.1    Schliep, A.2
  • 12
    • 77952309223 scopus 로고    scopus 로고
    • Aparallel and incremental algorithm for efficient unique signature discovery on DNA databases
    • Lee,H.P. et al. (2010) Aparallel and incremental algorithm for efficient unique signature discovery on DNA databases. BMC Bioinformatics, 11, 132.
    • (2010) BMC Bioinformatics , vol.11 , pp. 132
    • Lee, H.P.1
  • 13
    • 33846102841 scopus 로고    scopus 로고
    • probeBase - an online resource for rRNA-targeted oligonucleotide probes: new features 2007
    • (Database issue)
    • Loy,A. et al. (2007) probeBase - an online resource for rRNA-targeted oligonucleotide probes: new features 2007. Nucleic Acids Res., 35 (Database issue), D800-D804.
    • (2007) Nucleic Acids Res , vol.35
    • Loy, A.1
  • 14
    • 51649116822 scopus 로고    scopus 로고
    • probeCheck - a central resource for evaluating oligonucleotide probe coverage and specificity
    • Loy,A. et al. (2008) probeCheck - a central resource for evaluating oligonucleotide probe coverage and specificity. Environ. Microbiol., 10, 2894-2898.
    • (2008) Environ. Microbiol. , vol.10 , pp. 2894-2898
    • Loy, A.1
  • 15
    • 34247592880 scopus 로고    scopus 로고
    • Improved 16S rRNA-targeted probe set for analysis of sulfate- reducing bacteria by fluorescence in situ hybridization
    • Lücker,S. et al. (2007) Improved 16S rRNA-targeted probe set for analysis of sulfate- reducing bacteria by fluorescence in situ hybridization. J. Microbiol. Methods, 69, 523-528.
    • (2007) J. Microbiol. Methods , vol.69 , pp. 523-528
    • Lücker, S.1
  • 16
    • 2542523843 scopus 로고    scopus 로고
    • ARB: a software environment for sequence data
    • Ludwig,W. 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
  • 17
    • 3142718885 scopus 로고    scopus 로고
    • Development and implementation of a parallel algorithm for the fast design of oligonucleotide probe sets for diagnostic DNA microarrays
    • Meier,H. et al. (2004) Development and implementation of a parallel algorithm for the fast design of oligonucleotide probe sets for diagnostic DNA microarrays. Concurr. Comput. Pract. Exper., 16, 873-893.
    • (2004) Concurr. Comput. Pract. Exper. , vol.16 , pp. 873-893
    • Meier, H.1
  • 18
    • 0028051148 scopus 로고
    • Oligonucleotide probe design-a new approach
    • Mitsuhashi,M. et al. (1994) Oligonucleotide probe design-a new approach. Nature, 367, 759-761.
    • (1994) Nature , vol.367 , pp. 759-761
    • Mitsuhashi, M.1
  • 19
    • 17444407072 scopus 로고    scopus 로고
    • YODA: selecting signature oligonucleotides
    • Nordberg,E.K. (2005) YODA: selecting signature oligonucleotides. Bioinformatics, 21, 1365-1370.
    • (2005) Bioinformatics , vol.21 , pp. 1365-1370
    • Nordberg, E.K.1
  • 20
    • 34249736359 scopus 로고    scopus 로고
    • Comprehensive DNA signature discovery and validation
    • Phillippy,A.M. et al. (2007) Comprehensive DNA signature discovery and validation. PLoS Comput. Biol., 3, e98.
    • (2007) PLoS Comput. Biol. , vol.3
    • Phillippy, A.M.1
  • 21
    • 67849101835 scopus 로고    scopus 로고
    • Insignia: a DNAsignature search web server for diagnostic assay development
    • Phillippy,A.M. et al. (2009) Insignia: a DNAsignature search web server for diagnostic assay development. Nucleic Acids Res., 37, W229-W234.
    • (2009) Nucleic Acids Res , vol.37
    • Phillippy, A.M.1
  • 22
    • 77949718257 scopus 로고    scopus 로고
    • Fasttree 2 approximately maximum-likelihood trees for large alignments
    • Price,M.N. et al. (2010) Fasttree 2 approximately maximum-likelihood trees for large alignments. PLoS One, 5, e9490.
    • (2010) PLoS One , vol.5
    • Price, M.N.1
  • 23
    • 37549027613 scopus 로고    scopus 로고
    • SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
    • Pruesse,E. et al. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res., 35, 7188-7196.
    • (2007) Nucleic Acids Res , vol.35 , pp. 7188-7196
    • Pruesse, E.1
  • 24
    • 1842508190 scopus 로고    scopus 로고
    • What does the future hold for clinical microbiology?
    • Raoult,D. et al. (2004) What does the future hold for clinical microbiology? Nat. Rev. Microbiol., 2, 151-159.
    • (2004) Nat. Rev. Microbiol. , vol.2 , pp. 151-159
    • Raoult, D.1
  • 25
    • 0038239283 scopus 로고    scopus 로고
    • OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach
    • Rouillard,J.-M. et al. (2003) OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res., 31, 3057-3062.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3057-3062
    • Rouillard, J.-M.1
  • 26
    • 0002890678 scopus 로고    scopus 로고
    • Nucleic acid probes and their application in environmental microbiology
    • Garrity,G. (ed.) Springer, New York
    • Schleifer,K. and Amann,R. (2001) Nucleic acid probes and their application in environmental microbiology. In Garrity,G. (ed.) Bergey's Manual of Systematic Bacteriology, Vol. 6289. Springer, New York, pp. 67-82.
    • (2001) Bergey's Manual of Systematic Bacteriology , vol.6289 , pp. 67-82
    • Schleifer, K.1    Amann, R.2
  • 27
    • 63849294654 scopus 로고    scopus 로고
    • 16S rRNA gene-based phylogenetic microarray for simultaneous identification of members of the genus Burkholderia
    • Schönmann,S. et al. (2009) 16S rRNA gene-based phylogenetic microarray for simultaneous identification of members of the genus Burkholderia. Environ. Microbiol., 11, 779-800.
    • (2009) Environ. Microbiol. , vol.11 , pp. 779-800
    • Schönmann, S.1
  • 28
    • 77249087837 scopus 로고    scopus 로고
    • ORMA:atoolforidentificationofspecies-specificvariations in 16S rRNA gene and oligonucleotides design
    • Severgnini,M. et al. (2009) ORMA:atoolforidentificationofspecies-specificvariations in 16S rRNA gene and oligonucleotides design. Nucleic Acids Res., 37, e109.
    • (2009) Nucleic Acids Res , vol.37
    • Severgnini, M.1
  • 29
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis,A. (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22, 2688-2690.
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 30
    • 33846429230 scopus 로고    scopus 로고
    • Rapid detection and identification of bacterial pathogens using novel molecular technologies: infection control and beyond
    • Tenover,F.C. (2007) Rapid detection and identification of bacterial pathogens using novel molecular technologies: infection control and beyond. Clin. Infect. Dis., 44, 418-423.
    • (2007) Clin. Infect. Dis. , vol.44 , pp. 418-423
    • Tenover, F.C.1
  • 31
    • 23144447636 scopus 로고    scopus 로고
    • OligoWiz 2.0-integrating sequence feature annotation into the design of microarray probes
    • Wernersson,R. and Nielsen,H.B. (2005) OligoWiz 2.0-integrating sequence feature annotation into the design of microarray probes. Nucleic Acids Res., 33, W611-W615.
    • (2005) Nucleic Acids Res , vol.33
    • Wernersson, R.1    Nielsen, H.B.2
  • 32
    • 0029859176 scopus 로고    scopus 로고
    • 16S rRNA gene probes for Deinococcus species
    • Wise,M.G. et al. (1996) 16S rRNA gene probes for Deinococcus species. Syst. Appl. Microbiol., 19, 365-369.
    • (1996) Syst. Appl. Microbiol. , vol.19 , pp. 365-369
    • Wise, M.G.1
  • 33
    • 51649092232 scopus 로고    scopus 로고
    • Systematic evaluation of single mismatch stability predictors for fluorescence in situ hybridization
    • Yilmaz,L.S. et al. (2008) Systematic evaluation of single mismatch stability predictors for fluorescence in situ hybridization. Environ. Microbiol., 10, 2872-2885.
    • (2008) Environ. Microbiol. , vol.10 , pp. 2872-2885
    • Yilmaz, L.S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.