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Volumn 15, Issue 1, 2014, Pages

Consistency of metagenomic assignment programs in simulated and real data

Author keywords

Assignment; Comparison; Metagenomics

Indexed keywords

LIFE CYCLE;

EID: 84899062597     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-90     Document Type: Article
Times cited : (15)

References (21)
  • 1
    • 77649200259 scopus 로고    scopus 로고
    • A primer on metagenomics
    • 10.1371/journal.pcbi.1000667, 2829047, 20195499
    • Wooley JC, Godzik A, Friedberg I. A primer on metagenomics. PLoS Comput Biol 2010, 6:e1000667. 10.1371/journal.pcbi.1000667, 2829047, 20195499.
    • (2010) PLoS Comput Biol , vol.6
    • Wooley, J.C.1    Godzik, A.2    Friedberg, I.3
  • 2
    • 84860672197 scopus 로고    scopus 로고
    • A comparative evaluation of sequence classification programs
    • 10.1186/1471-2105-13-92, 3428669, 22574964
    • Bazinet AL, Cummings MP. A comparative evaluation of sequence classification programs. BMC Bioinformatics 2012, 13:92. 10.1186/1471-2105-13-92, 3428669, 22574964.
    • (2012) BMC Bioinformatics , vol.13 , pp. 92
    • Bazinet, A.L.1    Cummings, M.P.2
  • 3
    • 79959326732 scopus 로고    scopus 로고
    • Discovering the unknown: improving detection of novel species and genera from short reads
    • 3085467, 21541181
    • Rosen GL, Polikar R, Caseiro DA, Essinger SD, Sokhansanj BA. Discovering the unknown: improving detection of novel species and genera from short reads. J Biomed Biotechnol 2011, 2011:495849. 3085467, 21541181.
    • (2011) J Biomed Biotechnol , vol.2011 , pp. 495849
    • Rosen, G.L.1    Polikar, R.2    Caseiro, D.A.3    Essinger, S.D.4    Sokhansanj, B.A.5
  • 5
    • 33847702910 scopus 로고    scopus 로고
    • MEGAN analysis of metagenomic data
    • 10.1101/gr.5969107, 1800929, 17255551
    • Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res 2007, 17:377-386. 10.1101/gr.5969107, 1800929, 17255551.
    • (2007) Genome Res , vol.17 , pp. 377-386
    • Huson, D.H.1    Auch, A.F.2    Qi, J.3    Schuster, S.C.4
  • 6
    • 79961139783 scopus 로고    scopus 로고
    • Classifying short genomic fragments from novel lineages using composition and homology
    • 10.1186/1471-2105-12-328, 3173459, 21827705
    • Parks DH, MacDonald NJ, Beiko RG. Classifying short genomic fragments from novel lineages using composition and homology. BMC Bioinformatics 2011, 12:328. 10.1186/1471-2105-12-328, 3173459, 21827705.
    • (2011) BMC Bioinformatics , vol.12 , pp. 328
    • Parks, D.H.1    MacDonald, N.J.2    Beiko, R.G.3
  • 7
    • 69549135124 scopus 로고    scopus 로고
    • Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
    • 10.1038/nmeth.1358, 2762791, 19648916
    • Brady A, Salzberg SL. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat Methods 2009, 6:673-676. 10.1038/nmeth.1358, 2762791, 19648916.
    • (2009) Nat Methods , vol.6 , pp. 673-676
    • Brady, A.1    Salzberg, S.L.2
  • 10
    • 79952937941 scopus 로고    scopus 로고
    • Variation in tropical reef symbiont metagenomes defined by secondary metabolism
    • 10.1371/journal.pone.0017897, 3062557, 21445351
    • Donia MS, Fricke WF, Ravel J, Schmidt EW. Variation in tropical reef symbiont metagenomes defined by secondary metabolism. PLoS One 2011, 6:e17897. 10.1371/journal.pone.0017897, 3062557, 21445351.
    • (2011) PLoS One , vol.6
    • Donia, M.S.1    Fricke, W.F.2    Ravel, J.3    Schmidt, E.W.4
  • 13
    • 54949137701 scopus 로고    scopus 로고
    • MetaSim: a sequencing simulator for genomics and metagenomics
    • 10.1371/journal.pone.0003373, 2556396, 18841204
    • Richter DC, Ott F, Auch AF, Schmid R, Huson DH. MetaSim: a sequencing simulator for genomics and metagenomics. PLoS One 2008, 3:e3373. 10.1371/journal.pone.0003373, 2556396, 18841204.
    • (2008) PLoS One , vol.3
    • Richter, D.C.1    Ott, F.2    Auch, A.F.3    Schmid, R.4    Huson, D.H.5
  • 14
    • 40549141418 scopus 로고    scopus 로고
    • Metagenomics: read length matters
    • 10.1128/AEM.02181-07, 2258652, 18192407
    • Wommack KE, Bhavsar J, Ravel J. Metagenomics: read length matters. Appl Environ Microbiol 2008, 74:1453-1463. 10.1128/AEM.02181-07, 2258652, 18192407.
    • (2008) Appl Environ Microbiol , vol.74 , pp. 1453-1463
    • Wommack, K.E.1    Bhavsar, J.2    Ravel, J.3
  • 15
    • 78651266519 scopus 로고    scopus 로고
    • Combining gene prediction methods to improve metagenomic gene annotation
    • 10.1186/1471-2105-12-20, 3042383, 21232129
    • Yok NG, Rosen GL. Combining gene prediction methods to improve metagenomic gene annotation. BMC Bioinformatics 2011, 12:20. 10.1186/1471-2105-12-20, 3042383, 21232129.
    • (2011) BMC Bioinformatics , vol.12 , pp. 20
    • Yok, N.G.1    Rosen, G.L.2
  • 16
    • 84884470145 scopus 로고    scopus 로고
    • A new method for extracting skin microbes allows metagenomic analysis of whole-deep skin
    • 10.1371/journal.pone.0074914, 3779245, 24073227
    • Garcia-Garcerà M, Garcia-Etxebarria K, Coscollà M, Latorre A, Calafell F. A new method for extracting skin microbes allows metagenomic analysis of whole-deep skin. PLoS One 2013, 8:e74914. 10.1371/journal.pone.0074914, 3779245, 24073227.
    • (2013) PLoS One , vol.8
    • Garcia-Garcerà, M.1    Garcia-Etxebarria, K.2    Coscollà, M.3    Latorre, A.4    Calafell, F.5
  • 19
    • 79952390994 scopus 로고    scopus 로고
    • Fast identification and removal of sequence contamination from genomic and metagenomic datasets
    • 10.1371/journal.pone.0017288, 3052304, 21408061
    • Schmieder R, Edwards R. Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS One 2011, 6:e17288. 10.1371/journal.pone.0017288, 3052304, 21408061.
    • (2011) PLoS One , vol.6
    • Schmieder, R.1    Edwards, R.2
  • 20
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • 10.1093/nar/25.17.3389, 146917, 9254694
    • Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.H.4    Zhang, Z.5    Miller, W.6    Lipman, D.J.7
  • 21
    • 84863304598 scopus 로고    scopus 로고
    • Vienna, Austria: R Foundation for Statistical Computing, R Core team
    • R Core team R: A Language and Environment for Statistical Computing 2012, Vienna, Austria: R Foundation for Statistical Computing, R Core team.
    • (2012) R: A Language and Environment for Statistical Computing


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.