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Volumn 40, Issue 1, 2012, Pages

Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; GUANINE;

EID: 84855258501     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1067     Document Type: Article
Times cited : (150)

References (50)
  • 6
    • 10344227692 scopus 로고    scopus 로고
    • Metagenomics: Application of genomics to uncultured microorganisms
    • Handelsman, J. (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev., 68, 669.
    • (2004) Microbiol. Mol. Biol. Rev. , vol.68 , pp. 669
    • Handelsman, J.1
  • 7
    • 23944495106 scopus 로고    scopus 로고
    • Metagenomics for studying unculturable microorganisms: Cutting the Gordian knot
    • Schloss, P.D. and Handelsman, J. (2005) Metagenomics for studying unculturable microorganisms: cutting the Gordian knot. Genome Biol., 6, 229.
    • (2005) Genome Biol. , vol.6 , pp. 229
    • Schloss, P.D.1    Handelsman, J.2
  • 11
    • 72949091232 scopus 로고    scopus 로고
    • Bacterial community variation in human body habitats across space and time
    • Costello, E.K., Lauber, C.L., Hamady, M., Fierer, N., Gordon, J.I. and Knight, R. (2009) Bacterial community variation in human body habitats across space and time. Science, 326, 1694.
    • (2009) Science , vol.326 , pp. 1694
    • Costello, E.K.1    Lauber, C.L.2    Hamady, M.3    Fierer, N.4    Gordon, J.I.5    Knight, R.6
  • 15
    • 70349993601 scopus 로고    scopus 로고
    • ShotgunFunctionalizeR: An R-package for functional comparison of metagenomes
    • Kristiansson, E., Hugenholtz, P. and Dalevi, D. (2009) ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes. Bioinformatics, 25, 2737.
    • (2009) Bioinformatics , vol.25 , pp. 2737
    • Kristiansson, E.1    Hugenholtz, P.2    Dalevi, D.3
  • 19
    • 0027059264 scopus 로고
    • Assessment of protein coding measures
    • Fickett, J.W. and Tung, C. (1992) Assessment of protein coding measures. Nucleic Acids Res., 20, 6441-6450. (Pubitemid 23052659)
    • (1992) Nucleic Acids Research , vol.20 , Issue.24 , pp. 6441-6450
    • Fickett, J.W.1    Tung, C.-S.2
  • 20
    • 34147132825 scopus 로고    scopus 로고
    • Identifying bacterial genes and endosymbiont DNA with Glimmer
    • DOI 10.1093/bioinformatics/btm009
    • Delcher, A.L., Bratke, K.A., Powers, E.C. and Salzberg, S.L. (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics, 23, 673-679. (Pubitemid 46554717)
    • (2007) Bioinformatics , vol.23 , Issue.6 , pp. 673-679
    • Delcher, A.L.1    Bratke, K.A.2    Powers, E.C.3    Salzberg, S.L.4
  • 21
    • 55449131166 scopus 로고    scopus 로고
    • Bioinformatics for whole-genome shotgun sequencing of microbial communities
    • Chen, K. and Pachter, L. (2005) Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput. Biol., 1, 106-12.
    • (2005) PLoS Comput. Biol. , vol.1 , pp. 106-12
    • Chen, K.1    Pachter, L.2
  • 23
    • 74049094093 scopus 로고    scopus 로고
    • The effect of sequencing errors on metagenomic gene prediction
    • Hoff, K.J. (2009) The effect of sequencing errors on metagenomic gene prediction. BMC Genomics, 10, 520.
    • (2009) BMC Genomics , vol.10 , pp. 520
    • Hoff, K.J.1
  • 24
    • 67849095415 scopus 로고    scopus 로고
    • Orphelia: Predicting genes in metagenomic sequencing reads
    • Hoff, K.J., Lingner, T., Meinicke, P. and Tech, M. (2009) Orphelia: predicting genes in metagenomic sequencing reads. Nucleic Acids Res., 37(Suppl. 2), W101-W105.
    • (2009) Nucleic Acids Res. , vol.37 , Issue.SUPPL. 2
    • Hoff, K.J.1    Lingner, T.2    Meinicke, P.3    Tech, M.4
  • 25
    • 59149090570 scopus 로고    scopus 로고
    • MetaGeneAnnotator: Detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes
    • Noguchi, H., Taniguchi, T. and Itoh, T. (2008) MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res., 15, 387-396.
    • (2008) DNA Res. , vol.15 , pp. 387-396
    • Noguchi, H.1    Taniguchi, T.2    Itoh, T.3
  • 26
    • 78651326786 scopus 로고    scopus 로고
    • FragGeneScan: Predicting genes in short and error-prone reads
    • Rho, M., Tang, H. and Ye, Y. (2010) FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res., 38, e191.
    • (2010) Nucleic Acids Res , vol.38
    • Rho, M.1    Tang, H.2    Ye, Y.3
  • 27
    • 78651266519 scopus 로고    scopus 로고
    • Combining gene prediction methods to improve metagenomic gene annotation
    • Yok, N.G. and Rosen, G.L. (2011) Combining gene prediction methods to improve metagenomic gene annotation. BMC Bioinformatics, 12, 20.
    • (2011) BMC Bioinformatics , vol.12 , pp. 20
    • Yok, N.G.1    Rosen, G.L.2
  • 28
    • 77955902981 scopus 로고    scopus 로고
    • Ab initio gene identification in metagenomic sequences
    • Zhu, W., Lomsadze, A. and Borodovsky, M. (2010) Ab initio gene identification in metagenomic sequences. Nucleic Acids Res., 38, e132.
    • (2010) Nucleic Acids Res , vol.38
    • Zhu, W.1    Lomsadze, A.2    Borodovsky, M.3
  • 29
    • 69549135124 scopus 로고    scopus 로고
    • Phymm and PhymmBL: Metagenomic phylogenetic classification with interpolated Markov models
    • Brady, A. and Salzberg, S.L. (2009) Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat. Methods, 6, 673-676.
    • (2009) Nat. Methods , vol.6 , pp. 673-676
    • Brady, A.1    Salzberg, S.L.2
  • 30
    • 62549109116 scopus 로고    scopus 로고
    • TACOA -Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach
    • Diaz, N.N., Krause, L., Goesmann, A., Niehaus, K. and Nattkemper, T.W. (2009) TACOA -Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinformatics, 10, 56.
    • (2009) BMC Bioinformatics , vol.10 , pp. 56
    • Diaz, N.N.1    Krause, L.2    Goesmann, A.3    Niehaus, K.4    Nattkemper, T.W.5
  • 31
    • 67649887316 scopus 로고    scopus 로고
    • SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences
    • Monzoorul Haque, M., Ghosh, T.S., Komanduri, D. and Mande, S.S. (2009) SOrt-ITEMS: sequence orthology based approach for improved taxonomic estimation of metagenomic sequences. Bioinformatics, 25, 1722.
    • (2009) Bioinformatics , vol.25 , pp. 1722
    • Monzoorul Haque, M.1    Ghosh, T.S.2    Komanduri, D.3    Mande, S.S.4
  • 33
    • 47249139915 scopus 로고    scopus 로고
    • CompostBin: A DNA composition-based algorithm for binning environmental shotgun reads
    • Springer
    • Chatterji, S., Yamazaki, I., Bai, Z. and Eisen, J. (2008) CompostBin: a DNA composition-based algorithm for binning environmental shotgun reads. Research in Computational Molecular Biology. Springer, pp. 17-28.
    • (2008) Research in Computational Molecular Biology , pp. 17-28
    • Chatterji, S.1    Yamazaki, I.2    Bai, Z.3    Eisen, J.4
  • 34
    • 77958605377 scopus 로고    scopus 로고
    • Clustering metagenomic sequences with interpolated Markov models
    • Kelley, D.R. and Salzberg, S.L. (2010) Clustering metagenomic sequences with interpolated Markov models. BMC Bioinformatics, 11, 544.
    • (2010) BMC Bioinformatics , vol.11 , pp. 544
    • Kelley, D.R.1    Salzberg, S.L.2
  • 35
    • 70449622882 scopus 로고    scopus 로고
    • Unsupervised statistical clustering of environmental shotgun sequences
    • Kislyuk, A., Bhatnagar, S., Dushoff, J. and Weitz, J.S. (2009) Unsupervised statistical clustering of environmental shotgun sequences. BMC Bioinformatics, 10, 316.
    • (2009) BMC Bioinformatics , vol.10 , pp. 316
    • Kislyuk, A.1    Bhatnagar, S.2    Dushoff, J.3    Weitz, J.S.4
  • 36
    • 67649884742 scopus 로고    scopus 로고
    • MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction
    • Hu, G., Guo, J., Liu, Y. and Zhu, H. (2009) MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction. Bioinformatics, 25, 1843-1845.
    • (2009) Bioinformatics , vol.25 , pp. 1843-1845
    • Hu, G.1    Guo, J.2    Liu, Y.3    Zhu, H.4
  • 39
    • 58449118337 scopus 로고    scopus 로고
    • The organization of the bacterial genome
    • Rocha, E.P.C. (2008) The organization of the bacterial genome. Annu. Rev. Genet., 42, 211-233.
    • (2008) Annu. Rev. Genet. , vol.42 , pp. 211-233
    • Rocha, E.P.C.1
  • 42
    • 58149178579 scopus 로고    scopus 로고
    • NCBI Reference Sequences: Current status, policy and new initiatives
    • Pruitt, K.D., Tatusova, T., Klimke, W. and Maglott, D.R. (2009) NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res., 37, D32.
    • (2009) Nucleic Acids Res. , vol.37
    • Pruitt, K.D.1    Tatusova, T.2    Klimke, W.3    Maglott, D.R.4
  • 43
    • 77956543003 scopus 로고    scopus 로고
    • Characteristics of 454 pyrosequencing dataenabling realistic simulation with flowsim
    • Balzer, S., Malde, K., Lanzén, A., Sharma, A. and Jonassen, I. (2010) Characteristics of 454 pyrosequencing dataenabling realistic simulation with flowsim. Bioinformatics, 26, i420.
    • (2010) Bioinformatics , vol.26
    • Balzer, S.1    Malde, K.2    Lanzén, A.3    Sharma, A.4    Jonassen, I.5
  • 44
    • 52649157765 scopus 로고    scopus 로고
    • Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
    • Dohm, J.C., Lottaz, C., Borodina, T. and Himmelbauer, H. (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res., 36, e105.
    • (2008) Nucleic Acids Res. , vol.36
    • Dohm, J.C.1    Lottaz, C.2    Borodina, T.3    Himmelbauer, H.4
  • 46
    • 53649106195 scopus 로고    scopus 로고
    • Next-generation DNA sequencing
    • Shendure, J. and Ji, H. (2008) Next-generation DNA sequencing. Nat. Biotechnol., 26, 1135-1145.
    • (2008) Nat. Biotechnol. , vol.26 , pp. 1135-1145
    • Shendure, J.1    Ji, H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.