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Volumn 13, Issue 6, 2012, Pages 728-742

Current opportunities and challenges in microbial metagenome analysis-A bioinformatic perspective

Author keywords

16S rRNA biodiversity; Binning; Bioinformatics; Genomic standards consortium; Metagenomics; Next generation sequencing

Indexed keywords


EID: 84869998312     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbs039     Document Type: Article
Times cited : (169)

References (140)
  • 1
    • 0008048504 scopus 로고
    • Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses
    • Lane DJ, Pace B, Olsen GJ, et al. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. ProcNatl Acad SciUSA 1985;82(20):6955-9.
    • (1985) ProcNatl Acad SciUSA , vol.82 , Issue.20 , pp. 6955-6959
    • Lane, D.J.1    Pace, B.2    Olsen, G.J.3
  • 2
    • 37549027613 scopus 로고    scopus 로고
    • SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
    • Pruesse E, Quast C, Knittel K, et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 2007;35(21):7188-96.
    • (2007) Nucleic Acids Res , vol.35 , Issue.21 , pp. 7188-7196
    • Pruesse, E.1    Quast, C.2    Knittel, K.3
  • 4
    • 23944525404 scopus 로고    scopus 로고
    • Computational improvements reveal great bacterial diversity and high metal toxicity in soil
    • Gans J, Wolinsky M, Dunbar J. Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 2005;309(5739):1387-90.
    • (2005) Science , vol.309 , Issue.5739 , pp. 1387-1390
    • Gans, J.1    Wolinsky, M.2    Dunbar, J.3
  • 5
    • 33747073504 scopus 로고    scopus 로고
    • Microbial diversity in the deep sea and the underexplored "rare biosphere"
    • Sogin ML, Morrison HG, Huber JA, et al. Microbial diversity in the deep sea and the underexplored "rare biosphere". ProcNatl Acad SciUSA 2006;103(32):12115-20.
    • (2006) ProcNatl Acad SciUSA , vol.103 , Issue.32 , pp. 12115-12120
    • Sogin, M.L.1    Morrison, H.G.2    Huber, J.A.3
  • 6
    • 53849104257 scopus 로고    scopus 로고
    • The rational exploration of microbial diversity
    • Quince C, Curtis TP, Sloan WT. The rational exploration of microbial diversity. ISMEJ 2008;2(10):997-1006.
    • (2008) ISMEJ , vol.2 , Issue.10 , pp. 997-1006
    • Quince, C.1    Curtis, T.P.2    Sloan, W.T.3
  • 7
    • 77955251092 scopus 로고    scopus 로고
    • Ironing out the wrinkles in the rare biosphere through improved OTU clustering
    • Huse SM, Welch DM, Morrison HG, Sogin ML. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. EnvironMicrobiol 2010;12(7):1889-98.
    • (2010) EnvironMicrobiol , vol.12 , Issue.7 , pp. 1889-1898
    • Huse, S.M.1    Welch, D.M.2    Morrison, H.G.3    Sogin, M.L.4
  • 8
    • 0028946084 scopus 로고
    • Phylogenetic identification and in situ detection of individual microbial cells without cultivation
    • Amann RI, Ludwig W, Schleifer KH. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 1995;59(1):143-69.
    • (1995) Microbiol Rev , vol.59 , Issue.1 , pp. 143-169
    • Amann, R.I.1    Ludwig, W.2    Schleifer, K.H.3
  • 9
    • 0242684409 scopus 로고    scopus 로고
    • Effect of signal compounds and incubation conditions on the culturability of freshwater bacterioplankton
    • Bruns A, Nubel U, Cypionka H, Overmann J. Effect of signal compounds and incubation conditions on the culturability of freshwater bacterioplankton. Appl EnvironMicrobiol 2003;69(4):1980-89.
    • (2003) Appl EnvironMicrobiol , vol.69 , Issue.4 , pp. 1980-1989
    • Bruns, A.1    Nubel, U.2    Cypionka, H.3    Overmann, J.4
  • 10
    • 29144494967 scopus 로고    scopus 로고
    • Microbial diversity in coastal subsurface sediments: a cultivation approach using various electron acceptors and substrate gradients
    • Köpke B, Wilms R, Engelen B, et al. Microbial diversity in coastal subsurface sediments: a cultivation approach using various electron acceptors and substrate gradients. Appl EnvironMicrobiol 2005;71(12):7819-30.
    • (2005) Appl EnvironMicrobiol , vol.71 , Issue.12 , pp. 7819-7830
    • Köpke, B.1    Wilms, R.2    Engelen, B.3
  • 11
    • 79953266898 scopus 로고    scopus 로고
    • Single-cell genomics
    • Kalisky T, Quake SR. Single-cell genomics. Nat Methods 2011;8(4):311-14.
    • (2011) Nat Methods , vol.8 , Issue.4 , pp. 311-314
    • Kalisky, T.1    Quake, S.R.2
  • 12
    • 0032192790 scopus 로고    scopus 로고
    • Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products
    • Handelsman J, Rondon MR, Brady SF, et al. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol S 1998;5(10):R245-9.
    • (1998) Chem Biol S , vol.5 , Issue.10
    • Handelsman, J.1    Rondon, M.R.2    Brady, S.F.3
  • 13
    • 23944495106 scopus 로고    scopus 로고
    • Metagenomics for studying unculturable microorganisms: cutting the Gordian knot
    • Schloss PD, Handelsman J. Metagenomics for studying unculturable microorganisms: cutting the Gordian knot. Genome Biol 2005;6(8):229.
    • (2005) Genome Biol , vol.6 , Issue.8 , pp. 229
    • Schloss, P.D.1    Handelsman, J.2
  • 14
    • 10944226351 scopus 로고    scopus 로고
    • Metagenomics: genomic analysis of microbial communities
    • Riesenfeld CS, Schloss PD, Handelsman J. Metagenomics: genomic analysis of microbial communities. AnnuRevGenet 2004;38:525-52.
    • (2004) AnnuRevGenet , vol.38 , pp. 525-552
    • Riesenfeld, C.S.1    Schloss, P.D.2    Handelsman, J.3
  • 15
    • 84856403295 scopus 로고    scopus 로고
    • The great screen anomaly-a new frontier in product discovery through functional metagenomics
    • Ekkers DM, Cretoiu MS, Kielak AM, Elsas JD. The great screen anomaly-a new frontier in product discovery through functional metagenomics. Appl Microbiol Biotechnol 2012;93(3):1005-20.
    • (2012) Appl Microbiol Biotechnol , vol.93 , Issue.3 , pp. 1005-1020
    • Ekkers, D.M.1    Cretoiu, M.S.2    Kielak, A.M.3    Elsas, J.D.4
  • 16
    • 79953210780 scopus 로고    scopus 로고
    • Metagenomic analyses: past and future trends
    • Simon C, Daniel R. Metagenomic analyses: past and future trends. Appl EnvironMicrobiol 2011;77(4):1153-61.
    • (2011) Appl EnvironMicrobiol , vol.77 , Issue.4 , pp. 1153-1161
    • Simon, C.1    Daniel, R.2
  • 17
    • 52649090774 scopus 로고    scopus 로고
    • An invitation to the marriage of metagenomics and metabolomics
    • Turnbaugh PJ, Gordon JI. An invitation to the marriage of metagenomics and metabolomics. Cell 2008;134(5):708-13.
    • (2008) Cell , vol.134 , Issue.5 , pp. 708-713
    • Turnbaugh, P.J.1    Gordon, J.I.2
  • 18
    • 79956287318 scopus 로고    scopus 로고
    • Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean
    • Shi Y, Tyson GW, Eppley JM, DeLong EF. Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. ISMEJ 2011;5(6): 999-1013.
    • (2011) ISMEJ , vol.5 , Issue.6 , pp. 999-1013
    • Shi, Y.1    Tyson, G.W.2    Eppley, J.M.3    DeLong, E.F.4
  • 19
    • 84860488672 scopus 로고    scopus 로고
    • Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom
    • Teeling H, Fuchs BM, Becher D, et al. Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science 2012; 336(6081):608-11.
    • (2012) Science , vol.336 , Issue.6081 , pp. 608-611
    • Teeling, H.1    Fuchs, B.M.2    Becher, D.3
  • 20
    • 57349141505 scopus 로고    scopus 로고
    • A bioinformatician's guide to metagenomics
    • Kunin V, Copeland A, Lapidus A, et al. A bioinformatician's guide to metagenomics. Microbiol Mol Biol Rev 2008;72(4): 557-78.
    • (2008) Microbiol Mol Biol Rev , vol.72 , Issue.4 , pp. 557-578
    • Kunin, V.1    Copeland, A.2    Lapidus, A.3
  • 21
    • 77649174627 scopus 로고    scopus 로고
    • Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group
    • Meyerdierks A, Kube M, Kostadinov I, et al. Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group. Environ Microbiol 2010;12(2):422-39.
    • (2010) Environ Microbiol , vol.12 , Issue.2 , pp. 422-439
    • Meyerdierks, A.1    Kube, M.2    Kostadinov, I.3
  • 22
    • 33750431080 scopus 로고    scopus 로고
    • Symbiosis insights through metagenomic analysis of a microbial consortium
    • Woyke T, Teeling H, Ivanova NN, et al. Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 2006;443(7114):950-5.
    • (2006) Nature , vol.443 , Issue.7114 , pp. 950-955
    • Woyke, T.1    Teeling, H.2    Ivanova, N.N.3
  • 23
    • 77954084359 scopus 로고    scopus 로고
    • Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains
    • Pena A, Teeling H, Huerta-Cepas J, et al. Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains. ISME J 2010;4(7): 882-95.
    • (2010) ISME J , vol.4 , Issue.7 , pp. 882-895
    • Pena, A.1    Teeling, H.2    Huerta-Cepas, J.3
  • 24
    • 65449134335 scopus 로고    scopus 로고
    • Assembling the marine metagenome, one cell at a time
    • Woyke T, Xie G, Copeland A, et al. Assembling the marine metagenome, one cell at a time. PLoS One 2009;4(4): e5299.
    • (2009) PLoS One , vol.4 , Issue.4
    • Woyke, T.1    Xie, G.2    Copeland, A.3
  • 25
    • 84860008730 scopus 로고    scopus 로고
    • Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of verrucomicrobia
    • Martinez-Garcia M, Brazel DM, Swan BK, et al. Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of verrucomicrobia. PLoS One 2012;7(4):e35314.
    • (2012) PLoS One , vol.7 , Issue.4
    • Martinez-Garcia, M.1    Brazel, D.M.2    Swan, B.K.3
  • 26
    • 84860831021 scopus 로고    scopus 로고
    • Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use
    • Kleiner M, Wentrup C, Lott C, et al. Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use. Proc Natl Acad SciUSA 2012;109(19):E1173-82.
    • (2012) Proc Natl Acad SciUSA , vol.109 , Issue.19
    • Kleiner, M.1    Wentrup, C.2    Lott, C.3
  • 27
    • 78049434937 scopus 로고    scopus 로고
    • Replicate or lie
    • Prosser JI. Replicate or lie. Environ Microbiol 2010;12(7): 1806-10.
    • (2010) Environ Microbiol , vol.12 , Issue.7 , pp. 1806-1810
    • Prosser, J.I.1
  • 28
    • 84856770811 scopus 로고    scopus 로고
    • Direct comparisons of illumina vs Roche 454 sequencing technologies on the same microbial community DNA sample
    • Luo C, Tsementzi D, Kyrpides N, et al. Direct comparisons of illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS One 2012; 7(2):e30087.
    • (2012) PLoS One , vol.7 , Issue.2
    • Luo, C.1    Tsementzi, D.2    Kyrpides, N.3
  • 29
    • 0000383912 scopus 로고
    • Pseudoreplication and the design of ecological field experiments
    • Hurlbert SH. Pseudoreplication and the design of ecological field experiments. EcolMonogr 1984;54(2):187-211.
    • (1984) EcolMonogr , vol.54 , Issue.2 , pp. 187-211
    • Hurlbert, S.H.1
  • 30
    • 79957984228 scopus 로고    scopus 로고
    • Replication, lies and lesser-known truths regarding experimental design in environmental microbiology
    • Lennon JT. Replication, lies and lesser-known truths regarding experimental design in environmental microbiology. EnvironMicrobiol 2011;13(6):1383-6.
    • (2011) EnvironMicrobiol , vol.13 , Issue.6 , pp. 1383-1386
    • Lennon, J.T.1
  • 31
    • 77955603295 scopus 로고    scopus 로고
    • Unlocking short read sequencing for metagenomics
    • Rodrigue S, Materna AC, Timberlake SC, et al. Unlocking short read sequencing for metagenomics. PLoS One 2010; 5(7):e11840.
    • (2010) PLoS One , vol.5 , Issue.7
    • Rodrigue, S.1    Materna, A.C.2    Timberlake, S.C.3
  • 32
    • 0033055062 scopus 로고    scopus 로고
    • The use of gene clusters to infer functional coupling
    • Overbeek R, Fonstein M, D'Souza M, et al. The use of gene clusters to infer functional coupling. ProcNatl Acad SciUSA 1999;96(6):2896-901.
    • (1999) ProcNatl Acad SciUSA , vol.96 , Issue.6 , pp. 2896-2901
    • Overbeek, R.1    Fonstein, M.2    D'Souza, M.3
  • 33
    • 0037398732 scopus 로고    scopus 로고
    • Missing genes in metabolic pathways: a comparative genomics approach
    • Osterman A, Overbeek R. Missing genes in metabolic pathways: a comparative genomics approach. Curr Opin Chem Biol 2003;7(2):238-51.
    • (2003) Curr Opin Chem Biol , vol.7 , Issue.2 , pp. 238-251
    • Osterman, A.1    Overbeek, R.2
  • 34
    • 41549103817 scopus 로고    scopus 로고
    • "Candidatus Cloacamonas acidaminovorans": genome sequence reconstruction provides a first glimpse of a new bacterial division
    • Pelletier E, Kreimeyer A, Bocs S, et al. "Candidatus Cloacamonas acidaminovorans": genome sequence reconstruction provides a first glimpse of a new bacterial division. J Bacteriol 2008;190(7):2572-9.
    • (2008) J Bacteriol , vol.190 , Issue.7 , pp. 2572-2579
    • Pelletier, E.1    Kreimeyer, A.2    Bocs, S.3
  • 35
    • 79251587455 scopus 로고    scopus 로고
    • Metagenomic discovery of biomass-degrading genes and genomes from cow rumen
    • Hess M, Sczyrba A, Egan R, et al. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 2011;331(6016):463-7.
    • (2011) Science , vol.331 , Issue.6016 , pp. 463-467
    • Hess, M.1    Sczyrba, A.2    Egan, R.3
  • 36
    • 33746531322 scopus 로고    scopus 로고
    • Genome of Rice Cluster I archaea-the key methane producers in the rice rhizosphere
    • Erkel C, Kube M, Reinhardt R, Liesack W. Genome of Rice Cluster I archaea-the key methane producers in the rice rhizosphere. Science 2006;313(5785):370-2.
    • (2006) Science , vol.313 , Issue.5785 , pp. 370-372
    • Erkel, C.1    Kube, M.2    Reinhardt, R.3    Liesack, W.4
  • 37
    • 84856659328 scopus 로고    scopus 로고
    • Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota
    • Iverson V, Morris RM, Frazar CD, et al. Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science 2012;335(6068): 587-90.
    • (2012) Science , vol.335 , Issue.6068 , pp. 587-590
    • Iverson, V.1    Morris, R.M.2    Frazar, C.D.3
  • 38
    • 84858863014 scopus 로고    scopus 로고
    • Individual genome assembly from complex community short-read metagenomic datasets
    • Luo C, Tsementzi D, Kyrpides NC, Konstantinidis KT. Individual genome assembly from complex community short-read metagenomic datasets. ISME J 2012;6(4): 898-901.
    • (2012) ISME J , vol.6 , Issue.4 , pp. 898-901
    • Luo, C.1    Tsementzi, D.2    Kyrpides, N.C.3    Konstantinidis, K.T.4
  • 39
    • 79952374428 scopus 로고    scopus 로고
    • Genovo: de novo assembly for metagenomes
    • Laserson J, Jojic V, Koller D. Genovo: de novo assembly for metagenomes. JComputBiol 2011;18(3):429-43.
    • (2011) JComputBiol , vol.18 , Issue.3 , pp. 429-443
    • Laserson, J.1    Jojic, V.2    Koller, D.3
  • 40
    • 79959422558 scopus 로고    scopus 로고
    • Meta-IDBA: a de novo assembler for metagenomic data
    • Peng Y, Leung HC, Yiu SM, Chin FY. Meta-IDBA: a de novo assembler for metagenomic data. Bioinformatics 2011; 27(13):i94-101.
    • (2011) Bioinformatics , vol.27 , Issue.13
    • Peng, Y.1    Leung, H.C.2    Yiu, S.M.3    Chin, F.Y.4
  • 42
    • 84861728077 scopus 로고    scopus 로고
    • A de novo metagenomic assembly program for shotgun DNA reads
    • Lai B, Ding R, Li Y, et al. A de novo metagenomic assembly program for shotgun DNA reads. Bioinformatics 2012;28: 1455-62.
    • (2012) Bioinformatics , vol.28 , pp. 1455-1462
    • Lai, B.1    Ding, R.2    Li, Y.3
  • 43
    • 80054896129 scopus 로고    scopus 로고
    • Bambus 2 scaffolding metagenomes
    • Koren S, Treangen TJ, Pop M. Bambus 2: scaffolding metagenomes. Bioinformatics 2011;27(21):2964-71.
    • (2011) Bioinformatics , vol.27 , Issue.21 , pp. 2964-2971
    • Koren, S.1    Treangen, T.J.2    Pop, M.3
  • 44
    • 19144370509 scopus 로고    scopus 로고
    • Metagenomics or megagenomics?
    • Handelsman J. Metagenomics or megagenomics? Nat Rev Microbiol 2005;3(6):457-8.
    • (2005) Nat Rev Microbiol , vol.3 , Issue.6 , pp. 457-458
    • Handelsman, J.1
  • 45
    • 35348968286 scopus 로고    scopus 로고
    • The human microbiome project
    • Turnbaugh PJ, Ley RE, Hamady M, et al. The human microbiome project. Nature 2007;449(7164):804-10.
    • (2007) Nature , vol.449 , Issue.7164 , pp. 804-810
    • Turnbaugh, P.J.1    Ley, R.E.2    Hamady, M.3
  • 46
    • 80052722544 scopus 로고    scopus 로고
    • Meeting report: the terabase metagenomics workshop and the vision of an earth microbiome project
    • Gilbert JA, Meyer F, Antonopoulos D, etal. Meeting report: the terabase metagenomics workshop and the vision of an earth microbiome project. Stand Genomic Sci 2010;3(3): 243-8.
    • (2010) Stand Genomic Sci , vol.3 , Issue.3 , pp. 243-248
    • Gilbert, J.A.1    Meyer, F.2    Antonopoulos, D.3
  • 47
    • 79959794996 scopus 로고    scopus 로고
    • The earth microbiome project: meeting report of the "1 EMP meeting on sample selection and acquisition"at Argonne National Laboratory October 6 2010
    • Gilbert JA, Meyer F, Jansson J, et al. The earth microbiome project: meeting report of the "1 EMP meeting on sample selection and acquisition"at Argonne National Laboratory October 6 2010. Stand Genomic Sci 2010;3(3):249-53.
    • (2010) Stand Genomic Sci , vol.3 , Issue.3 , pp. 249-253
    • Gilbert, J.A.1    Meyer, F.2    Jansson, J.3
  • 48
    • 74049094093 scopus 로고    scopus 로고
    • The effect of sequencing errors on metagenomic gene prediction
    • Hoff KJ. The effect of sequencing errors on metagenomic gene prediction. BMCGenomics 2009;10(1):520.
    • (2009) BMCGenomics , vol.10 , Issue.1 , pp. 520
    • Hoff, K.J.1
  • 49
    • 33750976398 scopus 로고    scopus 로고
    • MetaGene: prokaryotic gene finding from environmental genome shotgun sequences
    • Noguchi H, Park J, Takagi T. MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Res 2006;34(19):5623-30.
    • (2006) Nucleic Acids Res , vol.34 , Issue.19 , pp. 5623-5630
    • Noguchi, H.1    Park, J.2    Takagi, T.3
  • 50
    • 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, Itoh T. MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res 2008;15(6):387-96.
    • (2008) DNA Res , vol.15 , Issue.6 , pp. 387-396
    • Noguchi, H.1    Taniguchi, T.2    Itoh, T.3
  • 51
    • 44649090674 scopus 로고    scopus 로고
    • Gene prediction in metagenomic fragments: a large scale machine learning approach
    • Hoff KJ, Tech M, Lingner T, et al. Gene prediction in metagenomic fragments: a large scale machine learning approach. BMC Bioinformatics 2008;9(1):217.
    • (2008) BMC Bioinformatics , vol.9 , Issue.1 , pp. 217
    • Hoff, K.J.1    Tech, M.2    Lingner, T.3
  • 52
    • 67849095415 scopus 로고    scopus 로고
    • Orphelia: predicting genes in metagenomic sequencing reads
    • Hoff KJ, Lingner T, Meinicke P, Tech M. Orphelia: predicting genes in metagenomic sequencing reads. Nucleic Acids Res 2009;37(Web Server issue):W101-5.
    • (2009) Nucleic Acids Res , vol.37 , Issue.WEB SERVER ISSUE
    • Hoff, K.J.1    Lingner, T.2    Meinicke, P.3    Tech, M.4
  • 53
    • 78651326786 scopus 로고    scopus 로고
    • FragGeneScan: predicting genes in short and error-prone reads
    • Rho M, Tang H, Ye Y. FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res 2010;38(20): e191.
    • (2010) Nucleic Acids Res , vol.38 , Issue.20
    • Rho, M.1    Tang, H.2    Ye, Y.3
  • 55
    • 77953676254 scopus 로고    scopus 로고
    • Genetack: frameshift identification in protein-coding sequences by the Viterbi algorithm
    • Antonov I, Borodovsky M. Genetack: frameshift identification in protein-coding sequences by the Viterbi algorithm. J Bioinform Comput Biol 2010;8(3):535-51.
    • (2010) J Bioinform Comput Biol , vol.8 , Issue.3 , pp. 535-551
    • Antonov, I.1    Borodovsky, M.2
  • 56
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool. JMol Biol 1990;215(3):403-10.
    • (1990) JMol Biol , vol.215 , Issue.3 , pp. 403-410
    • Altschul, S.F.1    Gish, W.2    Miller, W.3
  • 57
    • 9144232912 scopus 로고    scopus 로고
    • UniProt: the universal protein knowledgebase
    • Apweiler R, Bairoch A, Wu CH, et al. UniProt: the universal protein knowledgebase. Nucleic Acids Res 2004; 32(Database issue):D115-9.
    • (2004) Nucleic Acids Res , vol.32 , Issue.DATABASE
    • Apweiler, R.1    Bairoch, A.2    Wu, C.H.3
  • 58
    • 34248583647 scopus 로고    scopus 로고
    • PhyloGena-a user-friendly system for automated phylogenetic annotation of unknown sequences
    • Hanekamp K, Bohnebeck U, Beszteri B, Valentin K. PhyloGena-a user-friendly system for automated phylogenetic annotation of unknown sequences. Bioinformatics 2007;23(7):793-801.
    • (2007) Bioinformatics , vol.23 , Issue.7 , pp. 793-801
    • Hanekamp, K.1    Bohnebeck, U.2    Beszteri, B.3    Valentin, K.4
  • 59
    • 0034992826 scopus 로고    scopus 로고
    • The closest BLAST hit is often not the nearest neighbor
    • Koski LB, Golding GB. The closest BLAST hit is often not the nearest neighbor. JMol Evol 2001;52(6):540-2.
    • (2001) JMol Evol , vol.52 , Issue.6 , pp. 540-542
    • Koski, L.B.1    Golding, G.B.2
  • 61
    • 79951535930 scopus 로고    scopus 로고
    • Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG
    • Mitra S, Rupek P, Richter DC, et al. Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG. BMC Bioinformatics 2011;12(Suppl. 1):S21.
    • (2011) BMC Bioinformatics , vol.12 , Issue.SUPPL. 1
    • Mitra, S.1    Rupek, P.2    Richter, D.C.3
  • 62
    • 34447513240 scopus 로고    scopus 로고
    • DarkHorse: a method for genomewide prediction of horizontal gene transfer
    • Podell S, Gaasterland T. DarkHorse: a method for genomewide prediction of horizontal gene transfer. Genome Biol S 2007;8(2):R16.
    • (2007) Genome Biol S , vol.8 , Issue.2
    • Podell, S.1    Gaasterland, T.2
  • 63
    • 0030925920 scopus 로고    scopus 로고
    • Pfam: a comprehensive database of protein domain families based on seed alignments
    • Sonnhammer EL, Eddy SR, Durbin R. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 1997;28(3):405-20.
    • (1997) Proteins , vol.28 , Issue.3 , pp. 405-420
    • Sonnhammer, E.L.1    Eddy, S.R.2    Durbin, R.3
  • 64
    • 42449162998 scopus 로고    scopus 로고
    • Phylogenetic classification of short environmental DNA fragments
    • Krause L, Diaz NN, Goesmann A, et al. Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res 2008;36(7):2230-9.
    • (2008) Nucleic Acids Res , vol.36 , Issue.7 , pp. 2230-2239
    • Krause, L.1    Diaz, N.N.2    Goesmann, A.3
  • 65
    • 74049132798 scopus 로고    scopus 로고
    • WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads
    • Gerlach W, Junemann S, Tille F, et al. WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinformatics 2009; 10:430.
    • (2009) BMC Bioinformatics , vol.10 , pp. 430
    • Gerlach, W.1    Junemann, S.2    Tille, F.3
  • 66
  • 67
    • 0037315735 scopus 로고    scopus 로고
    • Evolutionary implications of microbial genome tetranucleotide frequency biases
    • Pride DT, Meinersmann RJ, Wassenaar TM, Blaser MJ. Evolutionary implications of microbial genome tetranucleotide frequency biases. GenomeRes 2003;13(2):145-58.
    • (2003) GenomeRes , vol.13 , Issue.2 , pp. 145-158
    • Pride, D.T.1    Meinersmann, R.J.2    Wassenaar, T.M.3    Blaser, M.J.4
  • 68
    • 33845957530 scopus 로고    scopus 로고
    • Accurate phylogenetic classification of variable-length DNA fragments
    • McHardy AC, Martin HG, Tsirigos A, et al. Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods 2007;4(1):63-72.
    • (2007) Nat Methods , vol.4 , Issue.1 , pp. 63-72
    • McHardy, A.C.1    Martin, H.G.2    Tsirigos, A.3
  • 69
    • 0032526323 scopus 로고    scopus 로고
    • Oligonucleotide bias in Bacillus subtilis: general trends and taxonomic comparisons
    • Rocha EP, Viari A, Danchin A. Oligonucleotide bias in Bacillus subtilis: general trends and taxonomic comparisons. Nucleic Acids Res 1998;26(12):2971-80.
    • (1998) Nucleic Acids Res , vol.26 , Issue.12 , pp. 2971-2980
    • Rocha, E.P.1    Viari, A.2    Danchin, A.3
  • 70
    • 4344670204 scopus 로고    scopus 로고
    • Application of tetranucleotide frequencies for the assignment of genomic fragments
    • Teeling H, Meyerdierks A, Bauer M, et al. Application of tetranucleotide frequencies for the assignment of genomic fragments. EnvironMicrobiol 2004;6(9):938-47.
    • (2004) EnvironMicrobiol , vol.6 , Issue.9 , pp. 938-947
    • Teeling, H.1    Meyerdierks, A.2    Bauer, M.3
  • 71
    • 13244279471 scopus 로고    scopus 로고
    • Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns
    • Reva ON, Tummler B. Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns. BMC Bioinformatics 2004;5:90.
    • (2004) BMC Bioinformatics , vol.5 , pp. 90
    • Reva, O.N.1    Tummler, B.2
  • 72
    • 69549135124 scopus 로고    scopus 로고
    • Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
    • Brady A, Salzberg SL. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. NatMethods 2009;6(9):673-6.
    • (2009) NatMethods , vol.6 , Issue.9 , pp. 673-676
    • Brady, A.1    Salzberg, S.L.2
  • 73
    • 0034887748 scopus 로고    scopus 로고
    • Capturing whole-genome characteristics in short sequences using a naive Bayesian classifier
    • Sandberg R, Winberg G, Branden CI, et al. Capturing whole-genome characteristics in short sequences using a naive Bayesian classifier. Genome Res 2001;11(8):1404-9.
    • (2001) Genome Res , vol.11 , Issue.8 , pp. 1404-1409
    • Sandberg, R.1    Winberg, G.2    Branden, C.I.3
  • 74
    • 62549109116 scopus 로고    scopus 로고
    • TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach
    • Diaz NN, Krause L, Goesmann A, et al. TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinformatics 2009;10:56.
    • (2009) BMC Bioinformatics , vol.10 , pp. 56
    • Diaz, N.N.1    Krause, L.2    Goesmann, A.3
  • 75
    • 0242500968 scopus 로고    scopus 로고
    • Informatics for unveiling hidden genome signatures
    • Abe T, Kanaya S, Kinouchi M, et al. Informatics for unveiling hidden genome signatures. Genome Res 2003; 13(4):693-702.
    • (2003) Genome Res , vol.13 , Issue.4 , pp. 693-702
    • Abe, T.1    Kanaya, S.2    Kinouchi, M.3
  • 76
    • 33646569088 scopus 로고    scopus 로고
    • Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples
    • Abe T, Sugawara H, Kinouchi M, et al. Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples. DNA Res 2005;12(5):281-90.
    • (2005) DNA Res , vol.12 , Issue.5 , pp. 281-290
    • Abe, T.1    Sugawara, H.2    Kinouchi, M.3
  • 77
    • 38649143159 scopus 로고    scopus 로고
    • Using growing self-organising maps to improve the binning process in environmental whole-genome shotgun sequencing
    • Chan C-KK, Hsu AL, Tang S-L, Halgamuge SK. Using growing self-organising maps to improve the binning process in environmental whole-genome shotgun sequencing. J Biomed Biotechnol 2008;2008:513701.
    • (2008) J Biomed Biotechnol , vol.2008 , pp. 513701
    • Chan, C.-K.K.1    Hsu, A.L.2    Tang, S.-L.3    Halgamuge, S.K.4
  • 78
    • 43749109829 scopus 로고    scopus 로고
    • Binning sequences using very sparse labels within a metagenome
    • Chan CK, Hsu AL, Halgamuge SK, Tang SL. Binning sequences using very sparse labels within a metagenome. BMC Bioinformatics 2008;9(1):215.
    • (2008) BMC Bioinformatics , vol.9 , Issue.1 , pp. 215
    • Chan, C.K.1    Hsu, A.L.2    Halgamuge, S.K.3    Tang, S.L.4
  • 79
    • 47049115023 scopus 로고    scopus 로고
    • Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification
    • Martin C, Diaz NN, Ontrup J, Nattkemper TW. Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification. Bioinformatics 2008;24(14):1568-74.
    • (2008) Bioinformatics , vol.24 , Issue.14 , pp. 1568-1574
    • Martin, C.1    Diaz, N.N.2    Ontrup, J.3    Nattkemper, T.W.4
  • 80
    • 70350015324 scopus 로고    scopus 로고
    • Community-wide analysis of microbial genome sequence signatures
    • Dick GJ, Andersson AF, Baker BJ, et al. Community-wide analysis of microbial genome sequence signatures. Genome Biol 2009;10(8):R85.
    • (2009) Genome Biol , vol.10 , Issue.8
    • Dick, G.J.1    Andersson, A.F.2    Baker, B.J.3
  • 81
    • 79955071957 scopus 로고    scopus 로고
    • Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics
    • Weber M, Teeling H, Huang S, et al. Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics. ISME J 2011; 5(5):918-28.
    • (2011) ISME J , vol.5 , Issue.5 , pp. 918-928
    • Weber, M.1    Teeling, H.2    Huang, S.3
  • 84
    • 79957877228 scopus 로고    scopus 로고
    • A robust and accurate binning algorithm for metagenomic sequences with arbitrary species abundance ratio
    • Leung HCM, Yiu SM, Yang B, et al. A robust and accurate binning algorithm for metagenomic sequences with arbitrary species abundance ratio. Bioinformatics 2011;27(11): 1489-95.
    • (2011) Bioinformatics , vol.27 , Issue.11 , pp. 1489-1495
    • Leung, H.C.M.1    Yiu, S.M.2    Yang, B.3
  • 85
    • 70449622882 scopus 로고    scopus 로고
    • Unsupervised statistical clustering of environmental shotgun sequences
    • Kislyuk A, Bhatnagar S, Dushoff J, Weitz JS. Unsupervised statistical clustering of environmental shotgun sequences. BMC Bioinformatics 2009;10:316.
    • (2009) BMC Bioinformatics , vol.10 , pp. 316
    • Kislyuk, A.1    Bhatnagar, S.2    Dushoff, J.3    Weitz, J.S.4
  • 86
    • 79952425617 scopus 로고    scopus 로고
    • A novel abundance-based algorithm for binning metagenomic sequences using l-tuples
    • Wu YW, Ye Y. A novel abundance-based algorithm for binning metagenomic sequences using l-tuples. J Comput Biol 2011;18(3):523-34.
    • (2011) J Comput Biol , vol.18 , Issue.3 , pp. 523-534
    • Wu, Y.W.1    Ye, Y.2
  • 87
    • 79958167222 scopus 로고    scopus 로고
    • Mixture models for analysis of the taxonomic composition of metagenomes
    • Meinicke P, Asshauer KP, Lingner T. Mixture models for analysis of the taxonomic composition of metagenomes. Bioinformatics 2011;27(12):1618-24.
    • (2011) Bioinformatics , vol.27 , Issue.12 , pp. 1618-1624
    • Meinicke, P.1    Asshauer, K.P.2    Lingner, T.3
  • 88
    • 84855263243 scopus 로고    scopus 로고
    • Unveiling microbial life in the new deep-sea hypersaline Lake Thetis Part II: a metagenomic study
    • Ferrer M, Werner J, Chernikova TN, et al. Unveiling microbial life in the new deep-sea hypersaline Lake Thetis. Part II: a metagenomic study. Environ Microbiol 2011;14(1): 268-81.
    • (2011) Environ Microbiol , vol.14 , Issue.1 , pp. 268-281
    • Ferrer, M.1    Werner, J.2    Chernikova, T.N.3
  • 89
    • 45749132147 scopus 로고    scopus 로고
    • Habitat-lite: a GSC case study based on free text terms for environmental metadata
    • Hirschman L, Clark C, Cohen KB, et al. Habitat-lite: a GSC case study based on free text terms for environmental metadata. OMICS 2008;12(2):129-36.
    • (2008) OMICS , vol.12 , Issue.2 , pp. 129-136
    • Hirschman, L.1    Clark, C.2    Cohen, K.B.3
  • 90
    • 0043123037 scopus 로고    scopus 로고
    • mreps: efficient and flexible detection of tandem repeats in DNA
    • Kolpakov R, Bana G, Kucherov G. mreps: efficient and flexible detection of tandem repeats in DNA. Nucleic Acids Res 2003;31(13):3672-8.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3672-3678
    • Kolpakov, R.1    Bana, G.2    Kucherov, G.3
  • 91
    • 0034764307 scopus 로고    scopus 로고
    • SSAHA: a fast search method for large DNA databases
    • Ning Z, Cox AJ, Mullikin JC. SSAHA: a fast search method for large DNA databases. Genome Res 2001; 11(10):1725-9.
    • (2001) Genome Res , vol.11 , Issue.10 , pp. 1725-1729
    • Ning, Z.1    Cox, A.J.2    Mullikin, J.C.3
  • 92
    • 0032873141 scopus 로고    scopus 로고
    • Genomes OnLine Database (GOLD 1 0): a monitor of complete and ongoing genome projects world-wide
    • Kyrpides NC. Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide. Bioinformatics 1999;15(9):773-4.
    • (1999) Bioinformatics , vol.15 , Issue.9 , pp. 773-774
    • Kyrpides, N.C.1
  • 93
    • 0035161543 scopus 로고    scopus 로고
    • Genomes OnLine Database (GOLD): a monitor of genome projects world-wide
    • Bernal A, Ear U, Kyrpides N. Genomes OnLine Database (GOLD): a monitor of genome projects world-wide. Nucleic Acids Res 2001;29(1):126-7.
    • (2001) Nucleic Acids Res , vol.29 , Issue.1 , pp. 126-127
    • Bernal, A.1    Ear, U.2    Kyrpides, N.3
  • 94
    • 72949101201 scopus 로고    scopus 로고
    • A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
    • Wu D, Hugenholtz P, Mavromatis K, et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 2009;462(7276):1056-60.
    • (2009) Nature , vol.462 , Issue.7276 , pp. 1056-1060
    • Wu, D.1    Hugenholtz, P.2    Mavromatis, K.3
  • 95
    • 80051735813 scopus 로고    scopus 로고
    • Taxonomic classification of metagenomic shotgun sequences with CARMA3
    • Gerlach W, Stoye J. Taxonomic classification of metagenomic shotgun sequences with CARMA3. Nucleic Acids Res 2011;39(14):e91.
    • (2011) Nucleic Acids Res , vol.39 , Issue.14
    • Gerlach, W.1    Stoye, J.2
  • 96
    • 84858386965 scopus 로고    scopus 로고
    • Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition
    • Saeed I, Tang SL, Halgamuge SK. Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition. Nucleic Acids Res 2012; 40(5):e34.
    • (2012) Nucleic Acids Res , vol.40 , Issue.5
    • Saeed, I.1    Tang, S.L.2    Halgamuge, S.K.3
  • 97
    • 84861180216 scopus 로고    scopus 로고
    • Joint analysis of multiple metagenomic samples
    • Baran Y, Halperin E. Joint analysis of multiple metagenomic samples. PLoSComput Biol 2012;8(2):e1002373.
    • (2012) PLoSComput Biol , vol.8 , Issue.2
    • Baran, Y.1    Halperin, E.2
  • 98
    • 84856521514 scopus 로고    scopus 로고
    • Dirichlet multinomial mixtures: generative models for microbial metagenomics
    • Holmes I, Harris K, Quince C. Dirichlet multinomial mixtures: generative models for microbial metagenomics. PLoS One 2012;7(2):e30126.
    • (2012) PLoS One , vol.7 , Issue.2
    • Holmes, I.1    Harris, K.2    Quince, C.3
  • 99
    • 84863783885 scopus 로고    scopus 로고
    • Ecological structuring of bacterial and archaeal taxa in surface ocean waters
    • In press. Doi: 10.1111/j.1574-6941.2012.01357.x1111
    • Yilmaz P, Iversen MH, Hankeln W, et al. Ecological structuring of bacterial and archaeal taxa in surface ocean waters. FEMS Microbiol Ecol. In press. Doi: 10.1111/j.1574-6941.2012.01357.x.
    • FEMS Microbiol Ecol
    • Yilmaz, P.1    Iversen, M.H.2    Hankeln, W.3
  • 100
    • 0037478650 scopus 로고    scopus 로고
    • Complete genome sequence of the marine planctomycete Pirellula sp. strain 1
    • Glöckner FO, Kube M, Bauer M, et al. Complete genome sequence of the marine planctomycete Pirellula sp. strain 1. Proc Natl Acad Sci USA 2003;100(14):8298-303.
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.14 , pp. 8298-8303
    • Glöckner, F.O.1    Kube, M.2    Bauer, M.3
  • 101
    • 84555188306 scopus 로고    scopus 로고
    • The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals
    • Kotera M, Hirakawa M, Tokimatsu T, et al. The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals. MethodsMol Biol 2012;802:19-39.
    • (2012) MethodsMol Biol , vol.802 , pp. 19-39
    • Kotera, M.1    Hirakawa, M.2    Tokimatsu, T.3
  • 103
    • 33846113652 scopus 로고    scopus 로고
    • TIGRFAMs and genome properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
    • Selengut JD, Haft DH, Davidsen T, et al. TIGRFAMs and genome properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res 2007;35(Database issue):D260-64.
    • (2007) Nucleic Acids Res , vol.35 , Issue.DATABASE
    • Selengut, J.D.1    Haft, D.H.2    Davidsen, T.3
  • 104
    • 0030854739 scopus 로고    scopus 로고
    • tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
    • Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997;25(5):955-64.
    • (1997) Nucleic Acids Res , vol.25 , Issue.5 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 105
    • 34248531753 scopus 로고    scopus 로고
    • Locating proteins in the cell using TargetP SignalP and related tools
    • Emanuelsson O, Brunak S, von Heijne G, Nielsen H. Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2007;2(4):953-71.
    • (2007) Nat Protoc , vol.2 , Issue.4 , pp. 953-971
    • Emanuelsson, O.1    Brunak, S.2    von Heijne, G.3    Nielsen, H.4
  • 106
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
    • Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. JMol Biol S 2001;305(3):567-80.
    • (2001) JMol Biol S , vol.305 , Issue.3 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    von Heijne, G.3    Sonnhammer, E.L.4
  • 107
    • 0034888209 scopus 로고    scopus 로고
    • A novel tool for the prediction of transmembrane protein topology based on a statistical analysis of the SwissProt database: the OrienTM algorithm
    • Liakopoulos TD, Pasquier C, Hamodrakas SJ. A novel tool for the prediction of transmembrane protein topology based on a statistical analysis of the SwissProt database: the OrienTM algorithm. Protein Eng 2001;14(6): 387-90.
    • (2001) Protein Eng , vol.14 , Issue.6 , pp. 387-390
    • Liakopoulos, T.D.1    Pasquier, C.2    Hamodrakas, S.J.3
  • 108
    • 34447644810 scopus 로고    scopus 로고
    • CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats
    • Bland C, Ramsey TL, Sabree F, et al. CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 2007;8:209.
    • (2007) BMC Bioinformatics , vol.8 , pp. 209
    • Bland, C.1    Ramsey, T.L.2    Sabree, F.3
  • 109
    • 77950663547 scopus 로고    scopus 로고
    • CoBaltDB: complete bacterial and archaeal orfeomes subcellular localization database and associated resources
    • Goudenege D, Avner S, Lucchetti-Miganeh C, Barloy-Hubler F. CoBaltDB: complete bacterial and archaeal orfeomes subcellular localization database and associated resources. BMCMicrobiol 2010;10:88.
    • (2010) BMCMicrobiol , vol.10 , pp. 88
    • Goudenege, D.1    Avner, S.2    Lucchetti-Miganeh, C.3    Barloy-Hubler, F.4
  • 110
    • 33749646840 scopus 로고    scopus 로고
    • GNBSL: a new integrative system to predict the subcellular location for Gram-negative bacteria proteins
    • Guo J, Lin Y, Liu X. GNBSL: a new integrative system to predict the subcellular location for Gram-negative bacteria proteins. Proteomics 2006;6(19):5099-105.
    • (2006) Proteomics , vol.6 , Issue.19 , pp. 5099-5105
    • Guo, J.1    Lin, Y.2    Liu, X.3
  • 111
    • 19544388127 scopus 로고    scopus 로고
    • PSLpred: prediction of subcellular localization of bacterial proteins
    • Bhasin M, Garg A, Raghava GP. PSLpred: prediction of subcellular localization of bacterial proteins. Bioinformatics 2005;21(10):2522-4.
    • (2005) Bioinformatics , vol.21 , Issue.10 , pp. 2522-2524
    • Bhasin, M.1    Garg, A.2    Raghava, G.P.3
  • 112
    • 1942505330 scopus 로고    scopus 로고
    • Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions
    • Yu CS, Lin CJ, Hwang JK. Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions. Protein Sci 2004;13(5):1402-6.
    • (2004) Protein Sci , vol.13 , Issue.5 , pp. 1402-1406
    • Yu, C.S.1    Lin, C.J.2    Hwang, J.K.3
  • 113
    • 0042622254 scopus 로고    scopus 로고
    • PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria
    • Gardy JL, Spencer C, Wang K, et al. PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic Acids Res 2003;31(13): 3613-7.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3613-3617
    • Gardy, J.L.1    Spencer, C.2    Wang, K.3
  • 114
    • 78149297086 scopus 로고    scopus 로고
    • CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database
    • Park BH, Karpinets TV, Syed MH, et al. CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database. Glycobiology 2010;20(12):1574-84.
    • (2010) Glycobiology , vol.20 , Issue.12 , pp. 1574-1584
    • Park, B.H.1    Karpinets, T.V.2    Syed, M.H.3
  • 115
    • 78751650782 scopus 로고    scopus 로고
    • TSdb: a database of transporter substrates linking metabolic pathways and transporter systems on a genome scale via their shared substrates
    • Zhao M, Chen Y, Qu D, Qu H. TSdb: a database of transporter substrates linking metabolic pathways and transporter systems on a genome scale via their shared substrates. Sci China Life Sci 2011;54(1):60-4.
    • (2011) Sci China Life Sci , vol.54 , Issue.1 , pp. 60-64
    • Zhao, M.1    Chen, Y.2    Qu, D.3    Qu, H.4
  • 116
    • 33644873454 scopus 로고    scopus 로고
    • TCDB: the transporter classification database for membrane transport protein analyses and information
    • Saier MHJ, Tran CV, Barabote RD. TCDB: the transporter classification database for membrane transport protein analyses and information. Nucleic Acids Res 2006; 34(Database issue):D181-6.
    • (2006) Nucleic Acids Res , vol.34 , Issue.DATABASE
    • Saier, M.H.J.1    Tran, C.V.2    Barabote, R.D.3
  • 117
    • 58149202169 scopus 로고    scopus 로고
    • The transporter classification database: recent advances
    • Saier MHJ, Yen MR, Noto K, et al. The transporter classification database: recent advances. NucleicAcids Res 2009; 37(Database issue):D274-8.
    • (2009) NucleicAcids Res , vol.37 , Issue.DATABASE
    • Saier, M.H.J.1    Yen, M.R.2    Noto, K.3
  • 118
    • 80052606131 scopus 로고    scopus 로고
    • WebMGA: a customizable web server for fast metagenomic sequence analysis
    • Wu S, Zhu Z, Fu L, et al. WebMGA: a customizable web server for fast metagenomic sequence analysis. BMC Genomics 2011;12(1):444.
    • (2011) BMC Genomics , vol.12 , Issue.1 , pp. 444
    • Wu, S.1    Zhu, Z.2    Fu, L.3
  • 119
    • 33747881518 scopus 로고    scopus 로고
    • An experimental metagenome data management and analysis system
    • Markowitz VM, Ivanova N, Palaniappan K, et al. An experimental metagenome data management and analysis system. Bioinformatics 2006;22(14):e359-67.
    • (2006) Bioinformatics , vol.22 , Issue.14
    • Markowitz, V.M.1    Ivanova, N.2    Palaniappan, K.3
  • 120
    • 38549139537 scopus 로고    scopus 로고
    • IMG/M: a data management and analysis system for metagenomes
    • Markowitz VM, Ivanova NN, Szeto E, et al. IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res 2008;36(Database issue):D534-8.
    • (2008) Nucleic Acids Res , vol.36 , Issue.DATABASE
    • Markowitz, V.M.1    Ivanova, N.N.2    Szeto, E.3
  • 121
    • 84861898310 scopus 로고    scopus 로고
    • IMG/M: the integrated metagenome data management and comparative analysis system
    • Markowitz VM, Chen IM, Chu K, et al. IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res 2012;40(Database issue): D123-9.
    • (2012) Nucleic Acids Res , vol.40 , Issue.DATABASE
    • Markowitz, V.M.1    Chen, I.M.2    Chu, K.3
  • 122
    • 53549118607 scopus 로고    scopus 로고
    • The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes
    • Meyer F, Paarmann D, D'Souza M, et al. The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 2008;9(1):386.
    • (2008) BMC Bioinformatics , vol.9 , Issue.1 , pp. 386
    • Meyer, F.1    Paarmann, D.2    D'Souza, M.3
  • 124
    • 77957761759 scopus 로고    scopus 로고
    • METAREP: JCVI metagenomics reports-an open source tool for high-performance comparative metagenomics
    • Goll J, Rusch DB, Tanenbaum DM, et al. METAREP: JCVI metagenomics reports-an open source tool for high-performance comparative metagenomics. Bioinformatics 2010;26(20):2631-2.
    • (2010) Bioinformatics , vol.26 , Issue.20 , pp. 2631-2632
    • Goll, J.1    Rusch, D.B.2    Tanenbaum, D.M.3
  • 125
    • 77951945504 scopus 로고    scopus 로고
    • Identifying biologically relevant differences between metagenomic communities
    • Parks DH, Beiko RG. Identifying biologically relevant differences between metagenomic communities. Bioinformatics 2010;26(6):715-21.
    • (2010) Bioinformatics , vol.26 , Issue.6 , pp. 715-721
    • Parks, D.H.1    Beiko, R.G.2
  • 126
    • 79960030549 scopus 로고    scopus 로고
    • CoMet-a web server for comparative functional profiling of metagenomes
    • Lingner T, Asshauer KP, Schreiber F, Meinicke P. CoMet-a web server for comparative functional profiling of metagenomes. Nucleic Acids Res 2011;39(Web Server issue):W518-23.
    • (2011) Nucleic Acids Res , vol.39 , Issue.WEB SERVER ISSUE
    • Lingner, T.1    Asshauer, K.P.2    Schreiber, F.3    Meinicke, P.4
  • 127
    • 71749111168 scopus 로고    scopus 로고
    • Analysis and comparison of very large metagenomes with fast clustering and functional annotation
    • Li W. Analysis and comparison of very large metagenomes with fast clustering and functional annotation. BMC Bioinformatics 2009;10:359.
    • (2009) BMC Bioinformatics , vol.10 , pp. 359
    • Li, W.1
  • 128
    • 33947215475 scopus 로고    scopus 로고
    • CAMERA: a community resource for metagenomics
    • Seshadri R, Kravitz SA, Smarr L, et al. CAMERA: a community resource for metagenomics. PLoS Biol 2007; 5(3):e75.
    • (2007) PLoS Biol , vol.5 , Issue.3
    • Seshadri, R.1    Kravitz, S.A.2    Smarr, L.3
  • 129
    • 78651266825 scopus 로고    scopus 로고
    • Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource
    • Sun S, Chen J, Li W, et al. Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Res 2011; 39(Database issue):D546-51.
    • (2011) Nucleic Acids Res , vol.39 , Issue.DATABASE
    • Sun, S.1    Chen, J.2    Li, W.3
  • 130
    • 39049092823 scopus 로고    scopus 로고
    • A statistical toolbox for metagenomics: assessing functional diversity in microbial communities
    • Schloss P, Handelsman J. A statistical toolbox for metagenomics: assessing functional diversity in microbial communities. BMC Bioinformatics 2008;9(1):34.
    • (2008) BMC Bioinformatics , vol.9 , Issue.1 , pp. 34
    • Schloss, P.1    Handelsman, J.2
  • 131
    • 80052028523 scopus 로고    scopus 로고
    • The real cost of sequencing: higher than you think!
    • Sboner A, Mu XJ, Greenbaum D, et al. The real cost of sequencing: higher than you think!. Genome Biol 2011; 12(8):125.
    • (2011) Genome Biol , vol.12 , Issue.8 , pp. 125
    • Sboner, A.1    Mu, X.J.2    Greenbaum, D.3
  • 133
    • 43449108562 scopus 로고    scopus 로고
    • The minimum information about a genome sequence (MIGS) specification
    • Field D, Garrity G, Gray T, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008;26(5):541-7.
    • (2008) Nat Biotechnol , vol.26 , Issue.5 , pp. 541-547
    • Field, D.1    Garrity, G.2    Gray, T.3
  • 134
    • 79955749319 scopus 로고    scopus 로고
    • Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
    • Yilmaz P, Kottmann R, Field D, et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol 2011;29(5):415-20.
    • (2011) Nat Biotechnol , vol.29 , Issue.5 , pp. 415-420
    • Yilmaz, P.1    Kottmann, R.2    Field, D.3
  • 135
    • 45749154807 scopus 로고    scopus 로고
    • A standard MIGS/MIMS compliant XML schema: toward the development of the genomic contextual data markup language (GCDML)
    • New Orleans, LA22
    • Kottmann R, Gray T, Murphy S, et al. A standard MIGS/MIMS compliant XML schema: toward the development of the genomic contextual data markup language (GCDML). OMICS J Integr Biol 2008;12(2): 115-New Orleans, LA22.
    • (2008) OMICS J Integr Biol , vol.12 , Issue.2 , pp. 115
    • Kottmann, R.1    Gray, T.2    Murphy, S.3
  • 136
    • 80052969517 scopus 로고    scopus 로고
    • The genomic standards consortium: bringing standards to life for microbial ecology
    • Yilmaz P, Gilbert JA, Knight R, et al. The genomic standards consortium: bringing standards to life for microbial ecology. ISMEJ 2011;5(10):1565-7.
    • (2011) ISMEJ , vol.5 , Issue.10 , pp. 1565-1567
    • Yilmaz, P.1    Gilbert, J.A.2    Knight, R.3
  • 137
    • 84871047611 scopus 로고    scopus 로고
    • MetAMOS: a metagenomic assembly and analysis pipeline for AMOS
    • Treangen TJ, Koren S, Astrovskaya I, et al. MetAMOS: a metagenomic assembly and analysis pipeline for AMOS. Genome Biol 2011;12(Suppl 1):25.
    • (2011) Genome Biol , vol.12 , Issue.SUPPL. 1 , pp. 25
    • Treangen, T.J.1    Koren, S.2    Astrovskaya, I.3
  • 139
    • 80455164755 scopus 로고    scopus 로고
    • Characterizing and controlling the motion of ssDNA in a solid-state nanopore
    • Luan B, Martyna G, Stolovitzky G. Characterizing and controlling the motion of ssDNA in a solid-state nanopore. BiophysJ 2011;101(9):2214-22.
    • (2011) BiophysJ , vol.101 , Issue.9 , pp. 2214-2222
    • Luan, B.1    Martyna, G.2    Stolovitzky, G.3


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