메뉴 건너뛰기




Volumn 17, Issue 4, 2017, Pages 760-769

Evaluating and optimizing the performance of software commonly used for the taxonomic classification of DNA metabarcoding sequence data

Author keywords

DNA barcoding; DNA metabarcoding; rdp Na ve Bayesian Classifier; rtax; taxonomic assignment; utax

Indexed keywords

BAYES THEOREM; COMPUTER SIMULATION; DNA BARCODING; PROCEDURES; SOFTWARE;

EID: 85005983418     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12628     Document Type: Article
Times cited : (35)

References (48)
  • 1
    • 85006986456 scopus 로고    scopus 로고
    • Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard—a report from a May 23–24, 2016 workshop (Gothenburg, Sweden)
    • Abarenkov K, Adams RI, Laszlo I et al. (2016) Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard—a report from a May 23–24, 2016 workshop (Gothenburg, Sweden). MycoKeys, 16, 1.
    • (2016) MycoKeys , vol.16 , pp. 1
    • Abarenkov, K.1    Adams, R.I.2    Laszlo, I.3
  • 2
    • 84860672197 scopus 로고    scopus 로고
    • A comparative evaluation of sequence classification programs
    • Bazinet AL, Cummings MP (2012) A comparative evaluation of sequence classification programs. BMC Bioinformatics, 13, 1–13.
    • (2012) BMC Bioinformatics , vol.13 , pp. 1-13
    • Bazinet, A.L.1    Cummings, M.P.2
  • 3
    • 84986562973 scopus 로고    scopus 로고
    • Pollen DNA barcoding: current applications and future prospects
    • Bell KL, Brosi BJ, de Vere N et al. (2016) Pollen DNA barcoding: current applications and future prospects. Genome, 59, 1–12.
    • (2016) Genome , vol.59 , pp. 1-12
    • Bell, K.L.1    Brosi, B.J.2    de Vere, N.3
  • 4
    • 84943580979 scopus 로고    scopus 로고
    • Metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data
    • Bengtsson-Palme J, Hartmann M, Eriksson KM et al. (2015) Metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data. Molecular Ecology Resources, 15, 1403–1414.
    • (2015) Molecular Ecology Resources , vol.15 , pp. 1403-1414
    • Bengtsson-Palme, J.1    Hartmann, M.2    Eriksson, K.M.3
  • 7
    • 69549135124 scopus 로고    scopus 로고
    • Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
    • Brady A, Salzberg SL (2009) Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nature Methods, 6, 673–676.
    • (2009) Nature Methods , vol.6 , pp. 673-676
    • Brady, A.1    Salzberg, S.L.2
  • 8
    • 84956958206 scopus 로고    scopus 로고
    • Taxonomic characterization of honey bee (Apis mellifera) pollen foraging based on non-overlapping paired-end sequencing of nuclear ribosomal loci
    • Cornman RS, Otto CRV, Iwanowicz D, Pettis JS (2015) Taxonomic characterization of honey bee (Apis mellifera) pollen foraging based on non-overlapping paired-end sequencing of nuclear ribosomal loci. PLoS One, 10, e0145365.
    • (2015) PLoS One , vol.10
    • Cornman, R.S.1    Otto, C.R.V.2    Iwanowicz, D.3    Pettis, J.S.4
  • 10
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460–2461.
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 12
    • 85020608174 scopus 로고    scopus 로고
    • (accessed 6 January 2016)
    • Edgar RC (2015b) Validating taxonomy classifiers. Available at: www.drive5.com/usearch/manual/taxonomy_validation.html (accessed 6 January 2016).
    • (2015) Validating taxonomy classifiers
    • Edgar, R.C.1
  • 13
    • 85020608177 scopus 로고    scopus 로고
    • (accessed 6 January 2016)
    • Edgar RC (2015c) UTAX algorithm. Available at: http://www.drive5.com/usearch/manual/utax_algo.html (accessed 6 January 2016).
    • (2015) UTAX algorithm
    • Edgar, R.C.1
  • 14
    • 84962786717 scopus 로고    scopus 로고
    • How to limit false positives in environmental DNA and metabarcoding?
    • Ficetola GF, Taberlet P, Coissac E (2016) How to limit false positives in environmental DNA and metabarcoding? Molecular Ecology Resources, 16, 604–607.
    • (2016) Molecular Ecology Resources , vol.16 , pp. 604-607
    • Ficetola, G.F.1    Taberlet, P.2    Coissac, E.3
  • 15
  • 16
    • 84943229982 scopus 로고    scopus 로고
    • Using DNA metabarcoding to identify the floral composition of honey: a new tool for investigating honey bee foraging preferences
    • Hawkins J, de Vere N, Griffith A et al. (2015) Using DNA metabarcoding to identify the floral composition of honey: a new tool for investigating honey bee foraging preferences. PLoS One, 10, e0134735.
    • (2015) PLoS One , vol.10
    • Hawkins, J.1    de Vere, N.2    Griffith, A.3
  • 20
    • 84924247676 scopus 로고    scopus 로고
    • Evaluating multiplexed next generation sequencing as a method in palynology for mixed pollen samples
    • Keller A, Danner N, Grimmer G et al. (2015) Evaluating multiplexed next generation sequencing as a method in palynology for mixed pollen samples. Plant Biology, 17, 558–566.
    • (2015) Plant Biology , vol.17 , pp. 558-566
    • Keller, A.1    Danner, N.2    Grimmer, G.3
  • 21
    • 84923096062 scopus 로고    scopus 로고
    • Efficient and sensitive identification and quantification of airborne pollen using next generation DNA sequencing
    • Kraaijeveld K, De Weger LA, Garcia MV et al. (2015) Efficient and sensitive identification and quantification of airborne pollen using next generation DNA sequencing. Molecular Ecology Resources, 15, 8–16.
    • (2015) Molecular Ecology Resources , vol.15 , pp. 8-16
    • Kraaijeveld, K.1    De Weger, L.A.2    Garcia, M.V.3
  • 22
    • 42449162998 scopus 로고    scopus 로고
    • Phylogenetic classification of short environmental DNA fragments
    • Krause L, Diaz NN, Goesmann A et al. (2008) Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Research, 36, 2230–2239.
    • (2008) Nucleic Acids Research , vol.36 , pp. 2230-2239
    • Krause, L.1    Diaz, N.N.2    Goesmann, A.3
  • 23
    • 84949908582 scopus 로고    scopus 로고
    • Statistical approaches to account for false-positive errors in environmental DNA samples
    • Lahoz-Monfort JJ, Guillera-Arroita G, Tingley R (2016) Statistical approaches to account for false-positive errors in environmental DNA samples. Molecular Ecology Resources, 16, 673–685.
    • (2016) Molecular Ecology Resources , vol.16 , pp. 673-685
    • Lahoz-Monfort, J.J.1    Guillera-Arroita, G.2    Tingley, R.3
  • 24
    • 84869030635 scopus 로고    scopus 로고
    • CREST—classification resources for environmental sequence tags
    • Lanzén A, Jørgensen SL, Huson DH et al. (2012) CREST—classification resources for environmental sequence tags. PLoS One, 7, e49334.
    • (2012) PLoS One , vol.7
    • Lanzén, A.1    Jørgensen, S.L.2    Huson, D.H.3
  • 25
    • 84963701152 scopus 로고    scopus 로고
    • Characterization of pollen and bacterial community composition in brood provisions of a small carpenter bee
    • McFrederick QS, Rehan SM (2016) Characterization of pollen and bacterial community composition in brood provisions of a small carpenter bee. Molecular Ecology, 25, 2302–2311.
    • (2016) Molecular Ecology , vol.25 , pp. 2302-2311
    • McFrederick, Q.S.1    Rehan, S.M.2
  • 27
    • 84916234886 scopus 로고    scopus 로고
    • Improving ITS sequence data for identification of plant pathogenic fungi
    • Nilsson RH, Hyde KD, Pawłowska J et al. (2014) Improving ITS sequence data for identification of plant pathogenic fungi. Fungal Diversity, 67, 11–19.
    • (2014) Fungal Diversity , vol.67 , pp. 11-19
    • Nilsson, R.H.1    Hyde, K.D.2    Pawłowska, J.3
  • 28
    • 85020572525 scopus 로고
    • Columbus, Ohio, USA
    • Ohio Supercomputer Center (1987) Citation. Columbus, Ohio, USA. Available at: http://osc.edu/ark:/19495/f5s1ph73.
    • (1987) Citation
  • 29
    • 84946412300 scopus 로고    scopus 로고
    • Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities
    • Peabody MA, Van Rossum T, Lo R, Brinkman FSL (2015) Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities. BMC Bioinformatics, 16, 363.
    • (2015) BMC Bioinformatics , vol.16 , pp. 363
    • Peabody, M.A.1    Van Rossum, T.2    Lo, R.3    Brinkman, F.S.L.4
  • 30
    • 84860470994 scopus 로고    scopus 로고
    • Factors that affect large subunit ribosomal DNA amplicon sequencing studies of fungal communities: classification method, primer choice, and error
    • Porter TM, Golding GB (2012) Factors that affect large subunit ribosomal DNA amplicon sequencing studies of fungal communities: classification method, primer choice, and error. PLoS One, 7, e35749.
    • (2012) PLoS One , vol.7
    • Porter, T.M.1    Golding, G.B.2
  • 31
    • 68149089830 scopus 로고    scopus 로고
    • Community analysis of chronic wound bacteria using 16S rRNA gene-based pyrosequencing: impact of diabetes and antibiotics on chronic wound microbiota
    • Price LB, Liu CM, Melendez JH et al. (2009) Community analysis of chronic wound bacteria using 16S rRNA gene-based pyrosequencing: impact of diabetes and antibiotics on chronic wound microbiota. PLoS One, 4, e6462.
    • (2009) PLoS One , vol.4
    • Price, L.B.1    Liu, C.M.2    Melendez, J.H.3
  • 32
    • 84875104888 scopus 로고    scopus 로고
    • A DNA metabarcoding study of a primate dietary diversity and plasticity across its entire fragmented range
    • Quéméré E, Hibert F, Miquel C et al. (2013) A DNA metabarcoding study of a primate dietary diversity and plasticity across its entire fragmented range. PLoS One, 8, e58971.
    • (2013) PLoS One , vol.8
    • Quéméré, E.1    Hibert, F.2    Miquel, C.3
  • 34
    • 34248149943 scopus 로고    scopus 로고
    • Bold: the barcode of life data system
    • Ratnasingham S, Hebert PDN (2007) Bold: the barcode of life data system (http://www.barcodinglife.org). Molecular Ecology Notes, 7, 355–364.
    • (2007) Molecular Ecology Notes , vol.7 , pp. 355-364
    • Ratnasingham, S.1    Hebert, P.D.N.2
  • 36
    • 84937735841 scopus 로고    scopus 로고
    • Application of ITS2 metabarcoding to determine the provenance of pollen collected by honey bees in a field-crop dominated agroecosystem
    • Richardson RT, Lin C-H, Quijia JQ, Sponsler BD, Goodell K, Johnson RM (2015b) Application of ITS2 metabarcoding to determine the provenance of pollen collected by honey bees in a field-crop dominated agroecosystem. Applications in Plant Sciences, 3, 1400066.
    • (2015) Applications in Plant Sciences , vol.3 , pp. 1400066
    • Richardson, R.T.1    Lin, C.-H.2    Quijia, J.Q.3    Sponsler, B.D.4    Goodell, K.5    Johnson, R.M.6
  • 37
    • 84955172656 scopus 로고    scopus 로고
    • Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes
    • Salazar G, Cornejo-Castillo FM, Borrull E et al. (2015) Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes. Molecular Ecology, 24, 5692–5706.
    • (2015) Molecular Ecology , vol.24 , pp. 5692-5706
    • Salazar, G.1    Cornejo-Castillo, F.M.2    Borrull, E.3
  • 38
    • 84876532610 scopus 로고    scopus 로고
    • Database resources of the National Center for Biotechnology Information
    • Sayers EW, Barrett T, Benson DA et al. (2013) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 41, D8–D20.
    • (2013) Nucleic Acids Research , vol.41 , pp. D8-D20
    • Sayers, E.W.1    Barrett, T.2    Benson, D.A.3
  • 39
    • 84860241679 scopus 로고    scopus 로고
    • Screening mammal biodiversity using DNA from Leeches
    • Schnell IB, Thomsen PF, Wilkinson N et al. (2012) Screening mammal biodiversity using DNA from Leeches. Current Biology, 22, 262–263.
    • (2012) Current Biology , vol.22 , pp. 262-263
    • Schnell, I.B.1    Thomsen, P.F.2    Wilkinson, N.3
  • 40
    • 84937239051 scopus 로고    scopus 로고
    • Increased efficiency in identifying mixed pollen samples by meta-barcoding with a dual-indexing approach
    • Sickel W, Ankenbrand MJ, Grimmer G et al. (2015) Increased efficiency in identifying mixed pollen samples by meta-barcoding with a dual-indexing approach. BMC Ecology, 15, 1–9.
    • (2015) BMC Ecology , vol.15 , pp. 1-9
    • Sickel, W.1    Ankenbrand, M.J.2    Grimmer, G.3
  • 41
    • 84862631902 scopus 로고    scopus 로고
    • Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences
    • Soergel D, Neelendu Dey AW, Knight R, Brenner SE (2012) Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. The ISME Journal, 6, 1440–1444.
    • (2012) The ISME Journal , vol.6 , pp. 1440-1444
    • Soergel, D.1    Neelendu Dey, A.W.2    Knight, R.3    Brenner, S.E.4
  • 43
    • 84941808021 scopus 로고    scopus 로고
    • High-throughput monitoring of wild bee diversity and abundance via mitogenomics
    • Tang M, Hardman CJ, Ji Y et al. (2015) High-throughput monitoring of wild bee diversity and abundance via mitogenomics. Methods in Ecology and Evolution, 6, 1034–1043.
    • (2015) Methods in Ecology and Evolution , vol.6 , pp. 1034-1043
    • Tang, M.1    Hardman, C.J.2    Ji, Y.3
  • 45
    • 84958280498 scopus 로고    scopus 로고
    • Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding
    • Valentini A, Taberlet P, Miaud C et al. (2016) Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology, 25, 929–942.
    • (2016) Molecular Ecology , vol.25 , pp. 929-942
    • Valentini, A.1    Taberlet, P.2    Miaud, C.3
  • 46
    • 84960888359 scopus 로고    scopus 로고
    • What you need is what you eat? Prey selection by the bat Myotis daubentonii
    • Vesterinen EJ, Ruokolainen L, Wahlberg N et al. (2016) What you need is what you eat? Prey selection by the bat Myotis daubentonii. Molecular Ecology, 25, 1581–1594.
    • (2016) Molecular Ecology , vol.25 , pp. 1581-1594
    • Vesterinen, E.J.1    Ruokolainen, L.2    Wahlberg, N.3
  • 47
    • 34548293679 scopus 로고    scopus 로고
    • Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology, 73, 5261–5267.
    • (2007) Applied and Environmental Microbiology , vol.73 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 48
    • 81055156693 scopus 로고    scopus 로고
    • A brief survey on sequence classification
    • Xing Z, Pei J, Keogh E (2010) A brief survey on sequence classification. ACM SIGKDD Explorations, 12, 40–48.
    • (2010) ACM SIGKDD Explorations , vol.12 , pp. 40-48
    • Xing, Z.1    Pei, J.2    Keogh, E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.