Atlas RM, Bartha R: Microbial Ecology. Fundamentals and Applications. Redwood: Benjamin/Cummings; 1993.
Google Scholar
Whitman WB, Coleman DC, Wiebe WJ: Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 1998, 95(12):6578–6583. 10.1073/pnas.95.12.6578
Article
PubMed Central
CAS
PubMed
Google Scholar
Torsvik V, Ovreas L: Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 2002, 5(3):240–245. 10.1016/S1369-5274(02)00324-7
Article
CAS
PubMed
Google Scholar
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF: Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 2004, 428(6978):37–43. 10.1038/nature02340
Article
CAS
PubMed
Google Scholar
Gans J, Wolinsky M, Dunbar J: Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 2005, 309(5739):1387–1390. 10.1126/science.1112665
Article
CAS
PubMed
Google Scholar
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, et al.: Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437(7057):376–380.
PubMed Central
CAS
PubMed
Google Scholar
Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, Arrieta JM, Herndl GJ: Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci USA 2006, 103(32):12115–12120. 10.1073/pnas.0605127103
Article
PubMed Central
CAS
PubMed
Google Scholar
Edwards RA, Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, Peterson DM, Saar MO, Alexander S, Alexander EC Jr, Rohwer F: Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 2006, 7: 57. 10.1186/1471-2164-7-57
Article
PubMed Central
PubMed
Google Scholar
Roesch LF, Fulthorpe RR, Riva A, Casella G, Hadwin AK, Kent AD, Daroub SH, Camargo FA, Farmerie WG, Triplett EW: Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 2007, 1(4):283–290.
PubMed Central
CAS
PubMed
Google Scholar
Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R: Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods 2008, 5(3):235–237. 10.1038/nmeth.1184
Article
PubMed Central
CAS
PubMed
Google Scholar
Bråte J, Logares R, Berney C, Ree DK, Klaveness D, Jakobsen KS, Shalchian-Tabrizi K: Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA. ISME J 2010.
Google Scholar
Lopez-Garcia P, Moreira D: Tracking microbial biodiversity through molecular and genomic ecology. Res Microbiol 2008, 159(1):67–73. 10.1016/j.resmic.2007.11.019
Article
CAS
PubMed
Google Scholar
Yu Y, Breitbart M, McNairnie P, Rohwer F: FastGroupII: a web-based bioinformatics platform for analyses of large 16S rDNA libraries. BMC Bioinformatics 2006, 7: 57. 10.1186/1471-2105-7-57
Article
PubMed Central
PubMed
Google Scholar
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, et al.: The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 2009, 37(Database):D141–145. 10.1093/nar/gkn879
Article
PubMed Central
CAS
PubMed
Google Scholar
Schloss PD, Handelsman J: Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 2005, 71(3):1501–1506. 10.1128/AEM.71.3.1501-1506.2005
Article
PubMed Central
CAS
PubMed
Google Scholar
Falgueras J, Lara AJ, Fernandez-Pozo N, Canton FR, Perez-Trabado G, Claros MG: SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read. BMC Bioinformatics 2010, 11: 38. 10.1186/1471-2105-11-38
Article
PubMed Central
PubMed
Google Scholar
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, et al.: QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010, 7(5):335–336. 10.1038/nmeth.f.303
Article
PubMed Central
CAS
PubMed
Google Scholar
SCATA - Sequence Clustering and Analysis of Tagged Amplicons[http://scata.mykopat.slu.se/]
Hartman AL, Riddle S, McPhillips T, Ludascher B, Eisen JA: Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences. BMC Bioinformatics 2010, 11: 317. 10.1186/1471-2105-11-317
Article
PubMed Central
PubMed
Google Scholar
Pandey RV, Nolte V, Schlotterer C: CANGS: a user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies. BMC Res Notes 2010, 3: 3. 10.1186/1756-0500-3-3
Article
PubMed Central
PubMed
Google Scholar
Giongo A, Crabb DB, Davis-Richardson AG, Chauliac D, Mobberley JM, Gano KA, Mukherjee N, Casella G, Roesch LF, Walts B, et al.: PANGEA: pipeline for analysis of next generation amplicons. ISME J 2010.
Google Scholar
Quince C, Lanzen A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF, Sloan WT: Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 2009, 6(9):639–641. 10.1038/nmeth.1361
Article
CAS
PubMed
Google Scholar
Pearson WR, Lipman DJ: Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988, 85(8):2444–2448. 10.1073/pnas.85.8.2444
Article
PubMed Central
CAS
PubMed
Google Scholar
Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM: Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 2007, 8(7):R143. 10.1186/gb-2007-8-7-r143
Article
PubMed Central
PubMed
Google Scholar
Tedersoo L, Nilsson RH, Abarenkov K, Jairus T, Sadam A, Saar I, Bahram M, Bechem E, Chuyong G, Koljalg U: 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. New Phytol 2010, 188(1):291–301. 10.1111/j.1469-8137.2010.03373.x
Article
CAS
PubMed
Google Scholar
Needleman SB, Wunsch CD: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970, 48(3):443–453. 10.1016/0022-2836(70)90057-4
Article
CAS
PubMed
Google Scholar
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389–3402. 10.1093/nar/25.17.3389
Article
PubMed Central
CAS
PubMed
Google Scholar
Huang Y, Niu B, Gao Y, Fu L, Li W: CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics 2010, 26(5):680–682. 10.1093/bioinformatics/btq003
Article
PubMed Central
CAS
PubMed
Google Scholar
Dickie IA: Insidious effects of sequencing errors on perceived diversity in molecular surveys. New Phytol 2010, 188(4):916–918. 10.1111/j.1469-8137.2010.03473.x
Article
PubMed
Google Scholar
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL: GenBank. Nucleic Acids Res 2008, 36(Database):D25–30.
Article
PubMed Central
CAS
PubMed
Google Scholar
Titan[http://hpc.uio.no/]
Kumar S, Skjaeveland A, Orr RJ, Enger P, Ruden T, Mevik BH, Burki F, Botnen A, Shalchian-Tabrizi K: AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses. BMC Bioinformatics 2009, 10: 357. 10.1186/1471-2105-10-357
Article
PubMed Central
PubMed
Google Scholar
Gardes M, Bruns TD: ITS primers with enhanced specificity for basidiomycetes--application to the identification of mycorrhizae and rusts. Mol Ecol 1993, 2(2):113–118. 10.1111/j.1365-294X.1993.tb00005.x
Article
CAS
PubMed
Google Scholar
White T, Bruns T, Lee S, Taylor J: Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR-protocols a guide to methods and applications. Edited by: Innis MA, Gelfand DH, Sninski JJ, White TJ. San Diego: Acedemic press; 1990:315–322.
Google Scholar
Binladen J, Gilbert MT, Bollback JP, Panitz F, Bendixen C, Nielsen R, Willerslev E: The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One 2007, 2(2):e197. 10.1371/journal.pone.0000197
Article
PubMed Central
PubMed
Google Scholar
van Orsouw NJ, Hogers RC, Janssen A, Yalcin F, Snoeijers S, Verstege E, Schneiders H, van der Poel H, van Oeveren J, Verstegen H, et al.: Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes. PLoS One 2007, 2(11):e1172. 10.1371/journal.pone.0001172
Article
PubMed Central
PubMed
Google Scholar
Huse SM, Welch DM, Morrison HG, Sogin ML: Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol 2010.
Google Scholar
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