Using the RDP classifier to predict taxonomic novelty and reduce the search space for finding novel organisms

PLoS ONE

Volumn 7, Issue 3, 2012, Pages

  Lan, Yemin ^a   Wang, Qiong ^b   Cole, James R ^a   Rosen, Gail L ^c  

^a DREXEL UNIVERSITY   (United States)

^b MICHIGAN STATE UNIVERSITY   (United States)

^c Drexel University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ACCURACY; ARTICLE; BAYES THEOREM; BOOTSTRAPPING; CLASSIFIER; GENUS; INTERMETHOD COMPARISON; PREDICTION; QUALITY CONTROL; RECEIVER OPERATING CHARACTERISTIC; RIBOSOMAL DATABASE PROJECT CLASSIFIER; SCORING SYSTEM; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; TAXONOMIC IDENTIFICATION; ARTIFICIAL INTELLIGENCE; BASE PAIRING; CLASSIFICATION; DISCRIMINANT ANALYSIS; GENETIC DATABASE; GENETICS; METAGENOMICS; METHODOLOGY; RIBOSOME; SOIL; STATISTICAL MODEL; TIME;

ARTIFICIAL INTELLIGENCE; BASE PAIRING; CLASSIFICATION; DATABASES, GENETIC; DISCRIMINANT ANALYSIS; LIKELIHOOD FUNCTIONS; METAGENOMICS; RIBOSOMES; ROC CURVE; SOIL; TIME FACTORS;

EID: 84863288435     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0032491     Document Type: Article

References (26)

1. Pace B, Stahl DA, Pace NR, (1984) The catalytic element of a ribosomal RNA-processing complex. J Biol Chem 259: 11454-11458.
2. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, et al. (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere" Proc Natl Acad Sci USA 103 (32): 12115-12120.
3. Lazarevic V, Whiteson K, Huse S, Hernandez D, Farinelli L, et al. (2009) Metagenomic study of the oral microbiota by Illumina high-throughput sequencing, Journal of Microbiological Methods 79 (3): 266-271.
4. Jones RT, Robeson MS, Lauber CL, Hamady M, Knight R, et al. (2009) A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses, ISME J 3 (4): 442-53.
5. Galand PE, Casamayor EO, Kirchman DL, Lovejoy C, (2009) Ecology of the rare microbial biosphere of the Arctic Ocean, Proc Natl Acad Sci USA 106 (52): 22427-22432.
6. Woo PCY, Lau SKP, Teng JLL, Tse H, Yuen KY, (2008) Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories, Clinical Microbiology and Infection 10: 908-34.
7. Janda JM, Abbott S, (2007) 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. Journal of Clinical Microbiology 45 (9): 2761-4.
8. Stackebrandt E, Ebers J, (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33: 152-5.
9. Mignard, Flandrois JP, (2006) 16S rRNA sequencing in routine bacterial identification: A 30-month experiment, Journal of Microbiological Methods 67 (3): 574-581.
10. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucl Acids Res 37 (suppl 1): D141-D145.
11. Wang Q, Garrity GM, Tiedje JM, Cole JR, (2007) Naive bayes classifier for rapid assignment of rrna sequences into the new bacterial taxonomy. Applied Environmental Microbiology 73 (16): 5261-5267.
12. Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, et al. (2008) Evolution of Mammals and Their Gut Microbes, Science 320 (5883): 1647-1651.
13. Zhang H, DiBaise JK, Zuccolo A, Kudrna D, Braidotti M, et al. (2009) Human gut microbiota in obesity and after gastric bypass. Proc Natl Acad Sci USA 106 (7): 2365-2370.
14. Ulrich A, Becker R, (2006) Soil parent material is a key determinant of the bacterial community structure in arable soils. FEMS Microbiology Ecology 56 (3): 430-443.
15. Biers EJ, Sun S, Howard EC, (2009) Prokaryotic Genomes and Diversity in Surface Ocean Waters: Interrogating the Global Ocean Sampling Metagenome. Appl Environ Microbiol 75: 2221-2229.
16. Rosen GL, Reichenberger ER, Rosenfeld A, (2011) NBC: The Naive Bayes Classification Tool Webserver for Taxonomic Classification of Metagenomic reads, Bioinformatics 27 (1): 127-129.
17. Brady A, Salzberg SL, (2009) Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nature Methods 6 (9): 673-676.
18. Sharpton TJ, Riesenfeld SJ, Kembel SW, Ladau J, O'Dwyer JP, et al. (2011) PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data. PLoS Comput Biol 7 (1).
19. Rosen GL, Polikar R, Caseiro DA, Essinger S, Sokhansanj B, (2011) Discovering the Unknown: Improving Detection of Novel Species and Genera from Short Reads, Journal of Biomedicine and Biotechnology Article ID 495849.
20. Sandberg R, Winberg G, Branden C-I, Kaske A, Ernberg I, et al. (2001) Capturing whole-genome characteristics in short sequences using a naive Bayesian classifier. Genome Res 11 (8): 1404-1409.
21. Rosen GL, Garbarine E, Caseiro D, Polikar R, Sokhansanj B, (2008) Metagenome fragment classification using N-mer frequency profiles. Advances in Bioinformatics Article ID 205969.
22. Li W, Godzik A, (2006) CD-HIT: a fast program for clustering and comparing large sets of protein or nucleotide sequences, Bioinformatics 22 (13): 1658-1659.
23. Navarette AA, Cannavan FS, Taketani RG, Tsai SM, (2010) "A Molecular Survey of the Diversity of Microbial Communities in Different Amazonian Agricultural Model Systems," Diversity 2: 787-809.
24. Li L, Hsiao WWL, Nandakumar R, Barbuto SM, Mongodin EF, et al. (2010) Analyzing Endodontic Infections by Deep Coverage Pyrosequencing. Journal of Dental Research 89 (9): 980-984.
25. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, et al. (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462: 1056-1060.
26. Peplies J, Kottmann R, Ludwig W, Glöckner FO, (2008) A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker gene. Syst Appl Microbiol 31: 251-257.