메뉴 건너뛰기




Volumn 56, Issue 2, 2014, Pages 78-84

TUIT, a BLAST-based tool for taxonomic classification of nucleotide sequences

Author keywords

Bioinformatics; Metagenome; Microbiome; Next generation sequencing; Software; Taxonomic classification

Indexed keywords

RNA 16S;

EID: 84893583895     PISSN: 07366205     EISSN: 19409818     Source Type: Journal    
DOI: 10.2144/000114135     Document Type: Article
Times cited : (13)

References (21)
  • 1
    • 84862173705 scopus 로고    scopus 로고
    • A core human microbiome as viewed through 16S rRNA sequence clusters
    • Huse, S.M., Y. Ye, Y. Zhou, and A.A. Fodor. 2012. A core human microbiome as viewed through 16S rRNA sequence clusters. PLoS ONE 7:e34242.
    • (2012) PLoS ONE , vol.7
    • Huse, S.M.1    Ye, Y.2    Zhou, Y.3    Fodor, A.A.4
  • 2
    • 53649106195 scopus 로고    scopus 로고
    • Next-generation DNA sequencing
    • Shendure, J. and H. Ji. 2008. Next-generation DNA sequencing. Nat. Biotechnol. 26:1135-1145.
    • (2008) Nat. Biotechnol , vol.26 , pp. 1135-1145
    • Shendure, J.1    Ji, H.2
  • 3
    • 34547834963 scopus 로고    scopus 로고
    • The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing
    • Binladen, J., M.T. Gilbert, J. P. Bollback, F. Panitz, C. Bendixen, R. Nielsen, and E. Willerslev. 2007. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS ONE 2:e197.
    • (2007) PLoS ONE , vol.2
    • Binladen, J.1    Gilbert, M.T.2    Bollback, J.P.3    Panitz, F.4    Bendixen, C.5    Nielsen, R.6    Willerslev, E.7
  • 5
    • 80053097826 scopus 로고    scopus 로고
    • Analysis of 16S rRNA amplicon sequencing options on the Roche/454 next-generation titanium sequencing platform
    • Tamaki, H., C.L. Wright, X. Li, Q. Lin, C. Hwang, S. Wang, J. Thimmapuram, Y. Kamagata, and W.T. Liu. 2011. Analysis of 16S rRNA amplicon sequencing options on the Roche/454 next-generation titanium sequencing platform. PLoS ONE 6:e25263.
    • (2011) PLoS ONE , vol.6
    • Tamaki, H.1    Wright, C.L.2    Li, X.3    Lin, Q.4    Hwang, C.5    Wang, S.6    Thimmapuram, J.7    Kamagata, Y.8    Liu, W.T.9
  • 6
    • 84355163066 scopus 로고    scopus 로고
    • Illumina-based analysis of microbial community diversity
    • Degnan, P.H., and H. Ochman. 2012. Illumina-based analysis of microbial community diversity. ISME J. 6:183-194.
    • (2012) ISME J , vol.6 , pp. 183-194
    • Degnan, P.H.1    Ochman, H.2
  • 7
    • 84979630690 scopus 로고    scopus 로고
    • PEAR: A fast and accurate Illumina Paired-End reAd mergeR
    • In press
    • Zhang, J., K. Kobert, T. Flouri, and A. Stamatakis. 2013. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics. (In press.)
    • (2013) Bioinformatics
    • Zhang, J.1    Kobert, K.2    Flouri, T.3    Stamatakis, A.4
  • 9
    • 34548293679 scopus 로고    scopus 로고
    • Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • Wang, Q., G. M. Garrity, J. M. Tiedje, and J.R. Cole. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73:5261-5267.
    • (2007) Appl. Environ. Microbiol , vol.73 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 10
    • 54549106898 scopus 로고    scopus 로고
    • Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrose-quencers
    • Liu, Z., T. Z. Desantis, G. L. Andersen, and R. Knight. 2008. Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrose-quencers. Nucleic Acids Res. 36:e120.
    • (2008) Nucleic Acids Res , vol.36
    • Liu, Z.1    Desantis, T.Z.2    Andersen, G.L.3    Knight, R.4
  • 12
  • 13
    • 0025259313 scopus 로고
    • Method s for assessing the statistica l significance of molecular sequence features by using general scoring schemes
    • Karlin, S. and S.F. Altschul. 1990. Method s for assessing the statistica l significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. USA 87:2264-2268.
    • (1990) Proc. Natl. Acad. Sci. USA , vol.87 , pp. 2264-2268
    • Karlin, S.1    Altschul, S.F.2
  • 14
    • 34147182303 scopus 로고    scopus 로고
    • A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria
    • Chakravorty, S., D. Helb, M. Burday, N. Connell, and D. Alland. 2007. A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J. Microbiol. Methods 69:330-339.
    • (2007) J. Microbiol. Methods , vol.69 , pp. 330-339
    • Chakravorty, S.1    Helb, D.2    Burday, M.3    Connell, N.4    Alland, D.5
  • 15
    • 40149103278 scopus 로고    scopus 로고
    • Error-correcting barcoded primers for pyrose-quencing hundreds of samples in multiplex
    • Hamady, M., J.J. Walker, J.K. Harris, N.J. Gold, and R. Knight. 2008. Error-correcting barcoded primers for pyrose-quencing hundreds of samples in multiplex. Nat. Methods 5:235-237.
    • (2008) Nat. Methods , vol.5 , pp. 235-237
    • Hamady, M.1    Walker, J.J.2    Harris, J.K.3    Gold, N.J.4    Knight, R.5
  • 18
    • 84856770811 scopus 로고    scopus 로고
    • Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample
    • Luo, C., D. Tsementzi, N. Kyrpides, T. Read, and K.T. Konstantinidis. 2012. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS ONE 7:e30087.
    • (2012) PLoS ONE , vol.7
    • Luo, C.1    Tsementzi, D.2    Kyrpides, N.3    Read, T.4    Konstantinidis, K.T.5
  • 19
    • 0032953638 scopus 로고    scopus 로고
    • Emended description of the order Chlamydiales, proposal of Parachlamyd iaceae fam. nov. and Simka ni-aceae fam. nov., each containing one monotypic genus, revised taxonomy of the family Chlamydiaceae, including a new genus and five new species, and standards for the identification of organisms
    • Everett, K.D., R.M. Bush, and A.A. Andersen. 1999. Emended description of the order Chlamydiales, proposal of Parachlamyd iaceae fam. nov. and Simka ni-aceae fam. nov., each containing one monotypic genus, revised taxonomy of the family Chlamydiaceae, including a new genus and five new species, and standards for the identification of organisms. Int. J. Syst. Bacteriol. 49:415-440.
    • (1999) Int. J. Syst. Bacteriol , vol.49 , pp. 415-440
    • Everett, K.D.1    Bush, R.M.2    Andersen, A.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.