Nucleic Acids Res 2007, 35:D169-D172.PubMedCrossRef 8. 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 Acid Res 2007, 35:7188–7196.PubMedCrossRef 9. Kanagawa T: Bias and artifacts in multitemplate Polymerase Chain Reactions (PCR). J Biosci Bioeng 2003, 96:317–323.PubMed 10. Marsh TL, Saxman P, Cole selleck J, Tiedje J: Terminal restriction fragment length polymorphism

analysis program, a web-based research tool for microbial community analysis. Appl Environ Microbiol 2000, 66:3616–3620.PubMedCrossRef 11. Shyu C, Soule T, Bent SJ, Foster JA, Forney LJ: MiCA: a web-based tool for the analysis of microbial communities based on terminal-restriction fragment length polymorphisms of 16S and 18S rRNA genes. Microb Ecol 2007, 53:562–570.PubMedCrossRef 12. Kent AD, Smith DJ, Benson BJ, Triplett EW: click here Web-based phylogenetic assignment tool for analysis of terminal restriction fragment length polymorphism profiles of microbial communities. Appl Environ Microbiol 2003, 69:6768–6776.PubMedCrossRef 13. Rösch C, Bothe H: Improved assessment of denitrifying, N 2 -fixing, and

total-community bacteria by terminal restriction fragment length polymorphism analysis using multiple restriction enzymes. Appl Environ Microbiol 2005, 71:2026–2035.PubMedCrossRef 14. Fitzjohn RG, Dickie IA: TRAMPR: an R package for analysis and matching of terminal-restriction fragment length polymorphism Methamphetamine (TRFLP) profiles. Mol Ecol Notes 2007, 7:583–587.CrossRef 15. Ricke P, Kolb S, Braker G: Application of a newly developed ARB software-integrated tool for in silico terminal restriction fragment length polymorphism analysis reveals the dominance of a novel pmoA cluster in a forest soil. Appl Environ Microbiol 2005, 71:1671–1673.PubMedCrossRef 16. Junier P, Junier T, Witzel KP: TRiFLe, a program

for in silico terminal restriction fragment length polymorphism analysis with user-defined sequence sets. Appl Environ Microbiol 2008, 74:6452–6456.PubMedCrossRef 17. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehväslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E: The bioperl toolkit: Perl modules for the life sciences. Genome Res 2002, 12:1611–1618.PubMedCrossRef 18. Rice P, Longden I, Bleasby A: EMBOSS: the European molecular biology open software suite. Trends Genet 2000, 16:276–277.PubMedCrossRef 19. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215:403–410.PubMed 20. Smith TF, Waterman MS: Identification of common molecular subsequences. J Mol Biol 1981, 147:195–197.PubMedCrossRef 21.