Tools for ribosomal RNA technology
| Tool | Description | Webpage | Citation |
|---|---|---|---|
| ARB | A software environment for sequence data |  www.arb-home.de | Ludwig, W., O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, A. Buchner, T. Lai, S. Steppi, G. Jobb, W. Forster, I. Brettske, S. Gerber, A. W. Ginhart, O. Gross, S. Grumann, S. Hermann, R. Jost, A. Konig, T. Liss, R. Lussmann, M. May, B. Nonhoff, B. Reichel, R. Strehlow, A. Stamatakis, N. Stuckmann, A. Vilbig, M. Lenke, T. Ludwig, A. Bode, and K. H. Schleifer. 2004. ARB: a software environment for sequence data. Nucleic Acid Res. 32: 1363-1371 |
| SILVA | Comprehensive, quality controlled and aligned ribosomal RNA sequence databases for all three domains of life | www.arb-silva.de | Pruesse, E., C. Quast, K. Knittel, B. Fuchs, W. Ludwig, J. Peplies, and F. O. Glöckner. 2007. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acid Res. 35: 7188-7196 |
| StrainInfo.net bioportal | Virtual catalogue providing integrated downstream information on microorganisms deposited within a global network of biological resource centers | www.straininfo.net | Dawyndt P, Vancanneyt M, De Meyer H, J. Swings. Knowledge accumulation and resolution of data inconsistencies during the integration of microbial information sources. IEEE Transactions on Knowledge and Data Engineering, 17: 1111-1126. |
| RDP II | The Ribosomal Database Project II | rdp.cme.msu.edu | Cole, J. R., Q. Wang, E. Cardenas, J. Fish, B. Chai, R. J. Farris, S. A. Kulam, D. M. McGarrell, T. Marsh, G. M. Garrity, and J. M. Tiedje. 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acid Res. 37:D141-145 |
| Greengenes | Ribosomal RNA database and data analysis tools | greengenes.lbl.gov | DeSantis, T.Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E.L., Keller, K., Huber, T., Dalevi, D., Hu, P. and Andersen, G.L. (2006) Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB, Appl Environ Microbiol, 72: 5069-5072 |
| STRING | Reference data of completely sequenced genomes, annotated with orthology and pathway information, plus protein network context | www.string-db.org | von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Krüger B, Snel B, Bork P. 2007. STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Res. 35: D358-62 |
| RAMI | A software for the identification and the visualization of microdiverse sequence clusters, based on patristic distances |
| Pommier, T., Canbäck, B., Lundberg, P., Hagström, Å and Tunlid, A. RAMI, a new tool to characterize microdiverse clusters in microbial communities: application to ribosomal DNA sequences from the marine environment. In preparation |
| (MICRO)-CARD-FISH | Microautoradiography combined with catalyzed reporter deposition fluorescence in situ hybridization with a cell permeabilization procedure particulary suited for Archaea | Teira, E., T. Reinthaler, A. Pernthaler, J. Pernthaler, G.J. Herndl, 2004: Combining catalyzed reporter deposition-fluorescence in situ hybridization and microautoradiography to detect substrate utilization by Bacteria and Archaea in the deep ocean. Appl. Environ. Microbiol., 70: 4411-4414 | |
| Q-MICRO-CARD-FISH | Quantification of single cell activity using microautoradiography combined with catalyzed reporter deposition fluorescence in situ hybridization and image analysis | Sintes, E., G.J. Herndl, 2006: Quantifying substrate uptake of individual cells of marine bacterioplankton by catalyzed reporter deposition fluorescence in situ hybridization combined with microautoradiography. Appl. Environ. Microbiol., 72: 7022-7028 | |
| BOLD | BOLD is a resource for the DNA barcode community | Sujeevan Ratnasingham and Paul D.N. Hebert - University of Guelph | |
| released 13. May 2008 |