메뉴 건너뛰기




Volumn 13, Issue 5, 2015, Pages 296-303

Web Resources for Metagenomics Studies

Author keywords

Metagenomes; Metagenomics; Software tools; Synthetic metagenome; Web resources

Indexed keywords

BIOINFORMATICS; COMPUTER PROGRAM; DATA ANALYSIS; METAGENOME; METAGENOMICS; PIPELINE; BIOLOGY; CLUSTER ANALYSIS; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; INFORMATION RETRIEVAL; INTERNET; PROCEDURES; SOFTWARE;

EID: 84949023743     PISSN: 16720229     EISSN: 22103244     Source Type: Journal    
DOI: 10.1016/j.gpb.2015.10.003     Document Type: Review
Times cited : (31)

References (38)
  • 1
    • 0032192790 scopus 로고    scopus 로고
    • Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products
    • Handelsman J., Rondon M.R., Brady S.F., Clardy J., Goodman R.M. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 1998, 5:R245-R249.
    • (1998) Chem Biol , vol.5 , pp. R245-R249
    • Handelsman, J.1    Rondon, M.R.2    Brady, S.F.3    Clardy, J.4    Goodman, R.M.5
  • 2
    • 19144366982 scopus 로고    scopus 로고
    • The metagenomics of soil
    • Daniel R. The metagenomics of soil. Nat Rev Microbiol 2005, 3:470-478.
    • (2005) Nat Rev Microbiol , vol.3 , pp. 470-478
    • Daniel, R.1
  • 3
    • 84862989346 scopus 로고    scopus 로고
    • Metagenomics - a guide from sampling to data analysis
    • Thomas T., Gilbert J., Meyer F. Metagenomics - a guide from sampling to data analysis. Microb Inform Exp 2012, 2:3.
    • (2012) Microb Inform Exp , vol.2 , pp. 3
    • Thomas, T.1    Gilbert, J.2    Meyer, F.3
  • 4
    • 84929409466 scopus 로고    scopus 로고
    • Bacterial tag encoded FLX titanium amplicon pyrosequencing (bTEFAP) based assessment of prokaryotic diversity in metagenome of Lonar soda lake, India
    • Dudhagara P., Ghelani A., Patel R., Chaudhari R., Bhatt S. Bacterial tag encoded FLX titanium amplicon pyrosequencing (bTEFAP) based assessment of prokaryotic diversity in metagenome of Lonar soda lake, India. Genom Data 2015, 4:8-11.
    • (2015) Genom Data , vol.4 , pp. 8-11
    • Dudhagara, P.1    Ghelani, A.2    Patel, R.3    Chaudhari, R.4    Bhatt, S.5
  • 5
    • 84929346378 scopus 로고    scopus 로고
    • Cultivation-independent comprehensive survey of bacterial diversity in Tulsi Shyam Hot Springs, India
    • Ghelani A., Patel R., Mangrola A., Dudhagara P. Cultivation-independent comprehensive survey of bacterial diversity in Tulsi Shyam Hot Springs, India. Genom Data 2015, 4:54-56.
    • (2015) Genom Data , vol.4 , pp. 54-56
    • Ghelani, A.1    Patel, R.2    Mangrola, A.3    Dudhagara, P.4
  • 6
    • 84934281104 scopus 로고    scopus 로고
    • Metagenomic data of fungal internal transcribed Spacer and 18S rRNA gene sequences from Lonar lake sediment, India
    • Dudhagara P., Ghelani A., Bhavsar S., Bhatt S. Metagenomic data of fungal internal transcribed Spacer and 18S rRNA gene sequences from Lonar lake sediment, India. Data Brief 2015, 4:266-268.
    • (2015) Data Brief , vol.4 , pp. 266-268
    • Dudhagara, P.1    Ghelani, A.2    Bhavsar, S.3    Bhatt, S.4
  • 7
    • 84878354100 scopus 로고    scopus 로고
    • Pearls and pitfalls of genomics-based microbiome analysis
    • Carlos N., Tang Y.W., Pei Z. Pearls and pitfalls of genomics-based microbiome analysis. Emerg Microbes Infect 2012, 1:e45.
    • (2012) Emerg Microbes Infect , vol.1 , pp. e45
    • Carlos, N.1    Tang, Y.W.2    Pei, Z.3
  • 9
    • 84922858689 scopus 로고    scopus 로고
    • Metagenomic sequence of saline desert microbiota from wild ass sanctuary, Little Rann of Kutch, Gujarat, India
    • Patel R., Mevada V., Prajapati D., Dudhagara P., Koringa P., Joshi C.G. Metagenomic sequence of saline desert microbiota from wild ass sanctuary, Little Rann of Kutch, Gujarat, India. Genom Data 2015, 3:137-139.
    • (2015) Genom Data , vol.3 , pp. 137-139
    • Patel, R.1    Mevada, V.2    Prajapati, D.3    Dudhagara, P.4    Koringa, P.5    Joshi, C.G.6
  • 10
    • 84929346377 scopus 로고    scopus 로고
    • Shotgun metagenomic sequencing based microbial diversity assessment of Lasundra hot spring, India
    • Mangrola A.V., Dudhagara P., Koringa P., Joshi C.G., Patel R.K. Shotgun metagenomic sequencing based microbial diversity assessment of Lasundra hot spring, India. Genom Data 2015, 4:73-75.
    • (2015) Genom Data , vol.4 , pp. 73-75
    • Mangrola, A.V.1    Dudhagara, P.2    Koringa, P.3    Joshi, C.G.4    Patel, R.K.5
  • 11
    • 58149505604 scopus 로고    scopus 로고
    • Discovering functional novelty in metagenomes: examples from light-mediated processes
    • Singh A.H., Doerks T., Letunic I., Raes J., Bork P. Discovering functional novelty in metagenomes: examples from light-mediated processes. J Bacteriol 2009, 191:32-41.
    • (2009) J Bacteriol , vol.191 , pp. 32-41
    • Singh, A.H.1    Doerks, T.2    Letunic, I.3    Raes, J.4    Bork, P.5
  • 12
    • 84929174408 scopus 로고    scopus 로고
    • CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers
    • Ounit R., Wanamaker S., Close T.J., Lonardi S. CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers. BMC Genomics 2015, 16:236.
    • (2015) BMC Genomics , vol.16 , pp. 236
    • Ounit, R.1    Wanamaker, S.2    Close, T.J.3    Lonardi, S.4
  • 14
    • 84921782403 scopus 로고    scopus 로고
    • The Amordad database engine for metagenomics
    • Behnam E., Smith A.D. The Amordad database engine for metagenomics. Bioinformatics 2014, 30:2949-2955.
    • (2014) Bioinformatics , vol.30 , pp. 2949-2955
    • Behnam, E.1    Smith, A.D.2
  • 15
    • 25644458211 scopus 로고    scopus 로고
    • The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
    • Overbeek R., Begley T., Butler R.M., Choudhuri J.V., Chuang H.Y., Cohoon M., et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 2005, 33:5691-5702.
    • (2005) Nucleic Acids Res , vol.33 , pp. 5691-5702
    • Overbeek, R.1    Begley, T.2    Butler, R.M.3    Choudhuri, J.V.4    Chuang, H.Y.5    Cohoon, M.6
  • 16
    • 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., Olson R., Glass E.M., Kubal M., et al. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 2008, 9:386.
    • (2008) BMC Bioinformatics , vol.9 , pp. 386
    • Meyer, F.1    Paarmann, D.2    D'Souza, M.3    Olson, R.4    Glass, E.M.5    Kubal, M.6
  • 17
    • 84891804612 scopus 로고    scopus 로고
    • The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
    • Overbeek R., Olson R., Pusch G.D., Olsen G.J., Davis J.J., Disz T., et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 2014, 42:D206-D214.
    • (2014) Nucleic Acids Res , vol.42 , pp. D206-D214
    • Overbeek, R.1    Olson, R.2    Pusch, G.D.3    Olsen, G.J.4    Davis, J.J.5    Disz, T.6
  • 24
    • 84863628126 scopus 로고    scopus 로고
    • IMG/M-HMP: a metagenome comparative analysis system for the human microbiome project
    • Markowitz V.M., Chen I.M., Chu K., Szeto E., Palaniappan K., Jacob B., et al. IMG/M-HMP: a metagenome comparative analysis system for the human microbiome project. PLoS One 2012, 7:e40151.
    • (2012) PLoS One , vol.7 , pp. e40151
    • Markowitz, V.M.1    Chen, I.M.2    Chu, K.3    Szeto, E.4    Palaniappan, K.5    Jacob, B.6
  • 25
    • 77957761759 scopus 로고    scopus 로고
    • METAREP: JCVI metagenomics reports - an open source tool for high-performance comparative metagenomics
    • Goll J., Rusch D.B., Tanenbaum D.M., Thiagarajan M., Li K., Methe B.A., et al. METAREP: JCVI metagenomics reports - an open source tool for high-performance comparative metagenomics. Bioinformatics 2010, 26:2631-2632.
    • (2010) Bioinformatics , vol.26 , pp. 2631-2632
    • Goll, J.1    Rusch, D.B.2    Tanenbaum, D.M.3    Thiagarajan, M.4    Li, K.5    Methe, B.A.6
  • 26
    • 84862184918 scopus 로고    scopus 로고
    • A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP)
    • Goll J., Thiagarajan M., Abubucker S., Huttenhower C., Yooseph S., Methé B.A. A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP). PLoS One 2012, 7:e29044.
    • (2012) PLoS One , vol.7 , pp. e29044
    • Goll, J.1    Thiagarajan, M.2    Abubucker, S.3    Huttenhower, C.4    Yooseph, S.5    Methé, B.A.6
  • 27
    • 79960030549 scopus 로고    scopus 로고
    • CoMet - a web server for comparative functional profiling of metagenomes
    • Lingner T., Asshauer K.P., Schreiber F., Meinicke P. CoMet - a web server for comparative functional profiling of metagenomes. Nucleic Acids Res 2011, 39:W518-W523.
    • (2011) Nucleic Acids Res , vol.39 , pp. W518-W523
    • Lingner, T.1    Asshauer, K.P.2    Schreiber, F.3    Meinicke, P.4
  • 28
    • 84864462144 scopus 로고    scopus 로고
    • METAGENassist: a comprehensive web server for comparative metagenomics
    • Arndt D., Xia J., Liu Y., Zhou Y., Guo A.C., Cruz J.A., et al. METAGENassist: a comprehensive web server for comparative metagenomics. Nucleic Acids Res 2012, 40:W88-W95.
    • (2012) Nucleic Acids Res , vol.40 , pp. W88-W95
    • Arndt, D.1    Xia, J.2    Liu, Y.3    Zhou, Y.4    Guo, A.C.5    Cruz, J.A.6
  • 29
    • 79961203060 scopus 로고    scopus 로고
    • MetaABC - an integrated metagenomics platform for data adjustment, binning and clustering
    • Su C.H., Hsu M.T., Wang T.Y., Chiang S., Cheng J.H., Weng F.C., et al. MetaABC - an integrated metagenomics platform for data adjustment, binning and clustering. Bioinformatics 2011, 27:2298-2299.
    • (2011) Bioinformatics , vol.27 , pp. 2298-2299
    • Su, C.H.1    Hsu, M.T.2    Wang, T.Y.3    Chiang, S.4    Cheng, J.H.5    Weng, F.C.6
  • 30
    • 84899824262 scopus 로고    scopus 로고
    • MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences
    • Luo C., Rodriguez-R L.M., Konstantinidis K.T. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014, 42:e73.
    • (2014) Nucleic Acids Res , vol.42 , pp. e73
    • Luo, C.1    Rodriguez-R, L.M.2    Konstantinidis, K.T.3
  • 31
    • 84876533577 scopus 로고    scopus 로고
    • MetaMicrobesOnline: phylogenomic analysis of microbial communities
    • Chivian D., Dehal P.S., Keller K., Arkin A.P. MetaMicrobesOnline: phylogenomic analysis of microbial communities. Nucleic Acids Res 2013, 41:D648-D654.
    • (2013) Nucleic Acids Res , vol.41 , pp. D648-D654
    • Chivian, D.1    Dehal, P.S.2    Keller, K.3    Arkin, A.P.4
  • 35
    • 78651266825 scopus 로고    scopus 로고
    • Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource
    • Sun S., Chen J., Li W., Altintas I., Lin A., Peltier S., et al. Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Res 2011, 39:D546-D551.
    • (2011) Nucleic Acids Res , vol.39 , pp. D546-D551
    • Sun, S.1    Chen, J.2    Li, W.3    Altintas, I.4    Lin, A.5    Peltier, S.6
  • 37
    • 84899552918 scopus 로고    scopus 로고
    • METAVIR 2: new tools for viral metagenome comparison and assembled virome analysis
    • Roux S., Tournayre J., Mahul A., Debroas D., Enault F. METAVIR 2: new tools for viral metagenome comparison and assembled virome analysis. BMC Bioinformatics 2014, 15:76.
    • (2014) BMC Bioinformatics , vol.15 , pp. 76
    • Roux, S.1    Tournayre, J.2    Mahul, A.3    Debroas, D.4    Enault, F.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.