A systematic search for discriminating sites in the 16S ribosomal RNA gene

Microbial Informatics and Experimentation

Volumn 4, Issue 1, 2014, Pages

  Vinje, Hilde ^a   Almøy, Trygve ^a   Liland, Kristian H ^a,b   Snipen, Lars ^a  

^a NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

^b NOFIMA   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ARTICLE; BACTERIAL GENETICS; ENTROPY; GENE LOCATION; GENETIC ALGORITHM; GENETIC CONSERVATION; GENETIC VARIABILITY; MARKER GENE; NONHUMAN; PHYLUM; PRIORITY JOURNAL; RNA ANALYSIS; RNA SEQUENCE; SEQUENCE ALIGNMENT;

PROKARYOTA;

EID: 84928537991     PISSN: None     EISSN: 20425783     Source Type: Journal    
DOI: 10.1186/2042-5783-4-2     Document Type: Article

References (30)

1. Woese CR, Stackebrand E, Macke TJ, Fox GE. A phylogenetic definition of the major eubacterial taxa. Syst Appl Microbiol 1985, 6:143-151. 10.1016/S0723-2020(85)80047-3, 11542017.
2. Woese CR. Bacterial evolution. Syst Appl Microbiol 1987, 51:221-271.
3. Pace NR. A molecular view of microbial diversity and the biosphere. Science 1997, 276:734-740. 10.1126/science.276.5313.734, 9115194.
4. Woese CR, Fox GE. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 1977, 74(11):5088-90. 10.1073/pnas.74.11.5088, 432104, 270744.
5. Harmsen D, Karch H. 16S rDNA for diagnosing pathogens: a living tree. ASM News 2004, 70:19-24.
6. Van de Peer Y, Chapelle S, . De Wachter R A quantitative map of nucleotide substitution rates in bacterial rRNA. Nucleic Acids Res 1996, 24:3381-3391. 10.1093/nar/24.17.3381, 146102, 8811093, De Wachter R.
7. Clarridge JE. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol 2004, 17:840-862.
8. Chakravorty S, Helb D, Burday M, Connell N, Alland D. A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J Microbiol Methods 2007, 69(2):330-339. 10.1016/j.mimet.2007.02.005, 2562909, 17391789.
9. Vasileiadis S, Puglisi E, Arena M, Cappa F, Cocconcelli PS, Trevisan M. Soil bacterial diversity screening using single 16S rRNA gene V regions coupled with multi-million read generating sequencing technologies. PLoS One 2012, 7(8):e42671. doi: 10.1371/journal.pone.0042671., 10.1371/journal.pone.0042671, 3412817, 22880076.
10. Bartlett JMS, Stirling D. A short history of the polymerase chain reaction. Methods Mol Biol 2003, 226:3-6.
11. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin L, Pace NR. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Nat Acad Sci 1985, 82:6955-6959. 10.1073/pnas.82.20.6955, 391288, 2413450.
12. Baker GC, Smith JJ, Cowan DA. Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 2003, 55:541-555. 10.1016/j.mimet.2003.08.009, 14607398.
13. Wang Y, Qian P. Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies. PLoS ONE 2009, 4(10):e7401. doi:10.1371/journal.pone.0007401., 10.1371/journal.pone.0007401, 2754607, 19816594.
14. Mao D, Zhou Q, Chen C, Quan Z. Coverage evaluation of universal bacterial primers using the metagenomic datasets. BMC Microbiol 2012, 12:66. 10.1186/1471-2180-12-66, 3445835, 22554309.
15. Winsley T, van Dorst JM, Brown MV, Ferrari BC. Capturing greater 16S rRNA gene sequence diversity within the domain bacteria. Appl Environ Microbiol 2012, 78:5938-5941. 10.1128/AEM.01299-12, 3406127, 22685133.
16. Cai L, Ye L, Tong AHY, Lok S, Zhang T. Biased diversity metrics revealed by bacterial 16S Pyrotags derived from different primer sets. PLoS ONE 2013, 8(1):e53649. doi:10.1371/journal.pone.0053649., 10.1371/journal.pone.0053649, 3544912, 23341963.
17. Mizrahi-Man O, Davenport ER, Gilad Y. Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs. PLoS ONE 2013, 8(1):e53608. doi:10.1371/journal.pone.0053608, 10.1371/journal.pone.0053608, 3538547, 23308262.
18. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, . Andersen G L Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006, 72:5069-5072. 10.1128/AEM.03006-05, 1489311, 16820507, Andersen G L.
19. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, . Tiedje J M The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 2008, 37:D141-D145. 2686447, 19004872, Tiedje J M.
20. Pruesse E, Quast C, Knittel K, Fuchs B, Ludwig W, Peplies J, Glöckner FO. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 2007, 35:7188-7196. 10.1093/nar/gkm864, 2175337, 17947321.
21. Greengenes database. [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi].
22. Ribosomal Database Project. [http://rdp.cme.msu.edu/].
23. SILVA database. [http://www.arb-silva.de/].
24. Wold S, Martens H, Wold H. The multivariate calibration problem in chemistry solved by the PLS method. Lect Notes Math 1983, 973:286-293.
25. Mehmood T, Martens H, Warringer J, Snipen L, . Sæbø S Mining for genotype-phenotype relations in Saccharomyces using partial least squares. BMC Bioinformatics 2011, 12:318. 10.1186/1471-2105-12-318, 3175482, 21812956, Sæbø S.
26. Mehmood T, Bohlin J, Kristoffersen AB, Warringer J, Snipen L, . Sæbø S Exploration of multivariate analysis in microbial coding sequence modeling. BMC Bioinformatics 2012, 13:97. 10.1186/1471-2105-13-97, 3473301, 22583558, Sæbø S.
27. Mehmood T, Liland KH, Snipen L, Sæbø S. A review of variable selection methods in partial least squares regression. Chemometrics Intell Lab Syst 2012, 118:62-69.
28. Rajalahti T, Arneberg R, Kroksveen AC, Berle M, Myhr KM, Kvalheim OM. Discriminating variable test and selectivity ratio plot: quantitative tools for interpretation and variable (biomarker) selection in complex spectral or chromatographic profiles. Anal Chem 2009, 81(7):2581-90. 10.1021/ac802514y, 19228047.
29. Nawrocki EP, Kolbe DL. Eddy SR: Infernal 1.0: inference of RNA alignments. Bioinformatics 2009, 25(10):1335-1337. 10.1093/bioinformatics/btp157, 2732312, 19307242.
30. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007, 73:5261-5267. 10.1128/AEM.00062-07, 1950982, 17586664.