메뉴 건너뛰기




Volumn 23, Issue 11, 2015, Pages 730-741

Ten years of maintaining and expanding a Microbial Genome and metagenome analysis system

Author keywords

Comparative genome analysis; Metagenomics; Microbial genomics

Indexed keywords

COMPUTER PROGRAM; DATA ANALYSIS; GENE CASSETTE; GENE CLUSTER; GENE EXPRESSION; GENE PRODUCT; GENETIC DATABASE; GENOMICS; HIGH THROUGHPUT SEQUENCING; INFORMATION PROCESSING; INTEGRATED MICROBIAL GENOMES SYSTEM; METAGENOME; MICROBIAL GENOME; MOLECULAR GENETICS; NONHUMAN; ORTHOLOGY; PHENOTYPE; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN MODIFICATION; PROTEIN PROTEIN INTERACTION; PROTEOMICS; REVIEW; SEARCH ENGINE; SYSTEM ANALYSIS; TRANSCRIPTOMICS; WEB BROWSER; BIOLOGY; CHEMICAL STRUCTURE; DATABASE MANAGEMENT SYSTEM; GENETICS; PROCEDURES; STATISTICS;

EID: 84960380093     PISSN: 0966842X     EISSN: 18784380     Source Type: Journal    
DOI: 10.1016/j.tim.2015.07.012     Document Type: Review
Times cited : (16)

References (37)
  • 2
    • 33747881518 scopus 로고    scopus 로고
    • An experimental metagenome data management and analysis system
    • Markowitz V., et al. An experimental metagenome data management and analysis system. Bioinformatics 2006, 22:e359-e367.
    • (2006) Bioinformatics , vol.22 , pp. e359-e367
    • Markowitz, V.1
  • 4
    • 84881138595 scopus 로고    scopus 로고
    • Insights into the phylogeny and coding potential of microbial dark matter
    • Rinke C., et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 2013, 499:431-437.
    • (2013) Nature , vol.499 , pp. 431-437
    • Rinke, C.1
  • 5
    • 84888774923 scopus 로고    scopus 로고
    • Genomes from metagenomics
    • Sharon I., Banfield J.F. Genomes from metagenomics. Science 2013, 342:1057-1058.
    • (2013) Science , vol.342 , pp. 1057-1058
    • Sharon, I.1    Banfield, J.F.2
  • 6
    • 84930816939 scopus 로고    scopus 로고
    • ProDeGe: a computational protocol for fully automated decontamination of genomes
    • Published online June 9, 2015
    • Tennessen K., et al. ProDeGe: a computational protocol for fully automated decontamination of genomes. ISME J. 2015, Published online June 9, 2015. 10.1038/ismej.2015.100.
    • (2015) ISME J.
    • Tennessen, K.1
  • 7
    • 84861898310 scopus 로고    scopus 로고
    • IMG: the integrated microbial genomes database and comparative analysis system
    • Markowitz V.M., et al. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res. 2012, 40:D115-D122.
    • (2012) Nucleic Acids Res. , vol.40 , pp. D115-D122
    • Markowitz, V.M.1
  • 8
    • 84891820094 scopus 로고    scopus 로고
    • IMG 4 version of the integrated microbial genomes comparative analysis system
    • Markowitz V.M., et al. IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res. 2014, 42:D560-D567.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D560-D567
    • Markowitz, V.M.1
  • 9
    • 84873739550 scopus 로고    scopus 로고
    • Improving microbial genome annotations in an integrated database context
    • Chen I.M.A., et al. Improving microbial genome annotations in an integrated database context. PLoS ONE 2013, 8:e54859.
    • (2013) PLoS ONE , vol.8
    • Chen, I.M.A.1
  • 10
    • 0042902833 scopus 로고    scopus 로고
    • The COG database: an updated version includes eukaryotes
    • Tatusov R.L., et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003, 4:41.
    • (2003) BMC Bioinformatics , vol.4 , pp. 41
    • Tatusov, R.L.1
  • 11
    • 84858077472 scopus 로고    scopus 로고
    • The Pfam protein families database
    • Punta M., et al. The Pfam protein families database. Nucleic Acids Res. 2012, 40:D290-D301.
    • (2012) Nucleic Acids Res. , vol.40 , pp. D290-D301
    • Punta, M.1
  • 12
    • 33846113652 scopus 로고    scopus 로고
    • TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
    • Selengut J.D., et al. TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res. 2007, 35:D260-D264.
    • (2007) Nucleic Acids Res. , vol.35 , pp. D260-D264
    • Selengut, J.D.1
  • 13
    • 84891760956 scopus 로고    scopus 로고
    • Data, information, knowledge and principle: back to metabolism in KEGG
    • Kanehisa M., et al. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 2014, 42:D199-D205.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D199-D205
    • Kanehisa, M.1
  • 14
    • 69949116874 scopus 로고    scopus 로고
    • IMG ER: a system for microbial annotation expert review and curation
    • Markowitz V.M., et al. IMG ER: a system for microbial annotation expert review and curation. Bioinformatics 2009, 25:2271-2278.
    • (2009) Bioinformatics , vol.25 , pp. 2271-2278
    • Markowitz, V.M.1
  • 15
    • 71049180352 scopus 로고    scopus 로고
    • Gene context analysis in the integrated microbial genomes (IMG) data management system
    • Mavromatis K., et al. Gene context analysis in the integrated microbial genomes (IMG) data management system. PLoS ONE 2009, 4:e7979.
    • (2009) PLoS ONE , vol.4
    • Mavromatis, K.1
  • 16
    • 84946041374 scopus 로고    scopus 로고
    • The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification
    • Reddy T.B.K., et al. The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification. Nucleic Acids Res. 2015, 43:D1099-D1106.
    • (2015) Nucleic Acids Res. , vol.43 , pp. D1099-D1106
    • Reddy, T.B.K.1
  • 17
    • 84939493603 scopus 로고    scopus 로고
    • IMG-ABC: A knowledge base to fuel discovery of biosynthetic gene clusters and novel secondary metabolites
    • Published online July 14, 2015
    • Hadjithomas M., et al. IMG-ABC: A knowledge base to fuel discovery of biosynthetic gene clusters and novel secondary metabolites. Mbio 2015, Published online July 14, 2015. 10.1128/mBio.00932-15.
    • (2015) Mbio
    • Hadjithomas, M.1
  • 18
    • 84876566794 scopus 로고    scopus 로고
    • ClusterMine360: a database of microbial PKS/NRPS biosynthesis
    • Conway K.R., Boddy C.N. ClusterMine360: a database of microbial PKS/NRPS biosynthesis. Nucleic Acids Res. 2013, 41:D402-D407.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D402-D407
    • Conway, K.R.1    Boddy, C.N.2
  • 19
    • 84876517188 scopus 로고    scopus 로고
    • DoBISCUIT: a database of secondary metabolite biosynthetic gene clusters
    • Ichikawa N., et al. DoBISCUIT: a database of secondary metabolite biosynthetic gene clusters. Nucleic Acids Res. 2013, 41:D408-D414.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D408-D414
    • Ichikawa, N.1
  • 20
    • 84904554933 scopus 로고    scopus 로고
    • Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters
    • Cimermancic P., et al. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell 2014, 158:412-421.
    • (2014) Cell , vol.158 , pp. 412-421
    • Cimermancic, P.1
  • 21
    • 84863628126 scopus 로고    scopus 로고
    • IMG/M-HMP: A metagenome comparative analysis system for the human microbiome project
    • Markowitz V.M., 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
    • Markowitz, V.M.1
  • 22
    • 77952299957 scopus 로고    scopus 로고
    • Prodigal: prokaryotic gene recognition and translation initiation site identification
    • Hyatt D., et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010, 11:119.
    • (2010) BMC Bioinformatics , vol.11 , pp. 119
    • Hyatt, D.1
  • 23
    • 33750976398 scopus 로고    scopus 로고
    • MetaGene: prokaryotic gene finding from environmental genome shotgun sequences
    • Hideki N., et al. MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Res. 2006, 34:5623-5630.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 5623-5630
    • Hideki, N.1
  • 24
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar R.C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26:2460-2461.
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 26
    • 43449108562 scopus 로고    scopus 로고
    • The minimum information about a genome sequence (MIGS) specification
    • Field D., et al. The minimum information about a genome sequence (MIGS) specification. Nat. Biotechnol. 2008, 26:541-547.
    • (2008) Nat. Biotechnol. , vol.26 , pp. 541-547
    • Field, D.1
  • 27
    • 84954147551 scopus 로고    scopus 로고
    • Genomic standards consortium projects
    • Field D., et al. Genomic standards consortium projects. Standards Genomic Sci. 2014, 9:599-601.
    • (2014) Standards Genomic Sci. , vol.9 , pp. 599-601
    • Field, D.1
  • 28
    • 84940594480 scopus 로고    scopus 로고
    • Toward a standard in structural genome annotation for prokaryotes
    • Published online July 25, 2015
    • Tripp H.J., et al. Toward a standard in structural genome annotation for prokaryotes. Standards Genomic Sci. 2015, Published online July 25, 2015. 10.1186/s40793-015-0034-9.
    • (2015) Standards Genomic Sci.
    • Tripp, H.J.1
  • 29
    • 84946034354 scopus 로고    scopus 로고
    • Microbial species delineation using whole genome sequences
    • Published online July 6, 2015
    • Varghese N., et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res. 2015, Published online July 6, 2015. 10.1093/nar/gkv657.
    • (2015) Nucleic Acids Res.
    • Varghese, N.1
  • 30
    • 84936942726 scopus 로고    scopus 로고
    • Unusual biology across a group comprising more that 15% of domain Bacteria
    • Published online June 15, 2015
    • Brown C., et al. Unusual biology across a group comprising more that 15% of domain Bacteria. Nature 2015, Published online June 15, 2015. 10.1038/nature14486.
    • (2015) Nature
    • Brown, C.1
  • 31
    • 27444438599 scopus 로고    scopus 로고
    • The microbial pan-genome
    • Medini D., et al. The microbial pan-genome. Curr. Opin. Genet. Dev. 2005, 15:589-594.
    • (2005) Curr. Opin. Genet. Dev. , vol.15 , pp. 589-594
    • Medini, D.1
  • 32
    • 53549118607 scopus 로고    scopus 로고
    • The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
    • Meyer F., 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
  • 33
    • 84891822499 scopus 로고    scopus 로고
    • EBI metagenomics - a new resource for the analysis and archiving of metagenomic data
    • Hunter S., et al. EBI metagenomics - a new resource for the analysis and archiving of metagenomic data. Nucleic Acids Res. 2014, 42:D600-D606.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D600-D606
    • Hunter, S.1
  • 34
    • 84977911640 scopus 로고    scopus 로고
    • Editorial The database revolution
    • Editorial The database revolution. Nature 2007, 445:229.
    • (2007) Nature , vol.445 , pp. 229
  • 35
    • 33751523045 scopus 로고    scopus 로고
    • Editorial Sustainable databases
    • Editorial Sustainable databases. Nat. Cell Biol. 2006, 8:1311.
    • (2006) Nat. Cell Biol. , vol.8 , pp. 1311
  • 36
    • 67650447476 scopus 로고    scopus 로고
    • Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream
    • Kyrpides N.C. Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream. Nat. Biotechnol. 2009, 27:627-632.
    • (2009) Nat. Biotechnol. , vol.27 , pp. 627-632
    • Kyrpides, N.C.1
  • 37
    • 84867450723 scopus 로고    scopus 로고
    • Databases fight funding cuts
    • Baker M. Databases fight funding cuts. Nature 2012, 489:19.
    • (2012) Nature , vol.489 , pp. 19
    • Baker, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.