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The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
Open accessAbstract
The Ribosomal Database Project (RDP) provides researchers with quality-controlled bacterial and archaeal small subunit rRNA alignments and analysis tools. An improved alignment strategy uses the Infernal secondary structure aware aligner to provide a more consistent higher quality alignment and faster processing of user sequences. Substantial new analysis features include a new Pyrosequencing Pipeline that provides tools to support analysis of ultra high-throughput rRNA sequencing data. This pipeline offers a collection of tools that automate the data processing and simplify the computationally intensive analysis of large sequencing libraries. In addition, a new Taxomatic visualization tool allows rapid visualization of taxonomic inconsistencies and suggests corrections, and a new class Assignment Generator provides instructors with a lesson plan and individualized teaching materials. Details about RDP data and analytical functions can be found at http://rdp.cme.msu.edu/.
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Research works printed but not linked: 19
- 2007, Nucleic Acids Research, 35, D169, 10.1093/nar/gkl889 · DOI
- Ashelford, 2005, Applied and Environmental Microbiology, 71, 7724, 10.1128/AEM.71.12.7724-7736.2005 · DOI
- Nawrocki, 2007, 3, e56, 10.1371/journal.pcbi.0030056 · DOI
- Griffiths-Jones, 2005, Nucleic Acids Research, 33, D121, 10.1093/nar/gki081 · DOI
- Ashelford, 2006, Applied and Environmental Microbiology, 72, 5734, 10.1128/AEM.00556-06 · DOI · Paper page
- 2007, Nucleic Acids Research, 35, 3100, 10.1093/nar/gkm160 · DOI
- Cannone, 2002, BMC bioinformatics [electronic resource], 3, 2, 10.1186/1471-2105-3-2 · DOI · Paper page
- 2001, BERGEYS MANUAL OF SYSTEMATIC BACTERIOLOGY, 1, 487
- 2007, Applied and Environmental Microbiology, 73, 3113, 10.1128/AEM.02012-06 · DOI · Paper page
- Sangwan, 2004, Applied and Environmental Microbiology, 70, 5875, 10.1128/AEM.70.10.5875-5881.2004 · DOI
- Harris, 2004, Applied and Environmental Microbiology, 70, 845, 10.1128/AEM.70.2.845-849.2004 · DOI
- 2007, Applied and Environmental Microbiology, 73, 5261, 10.1128/AEM.00062-07 · DOI · Paper page
- Smith, 2007, Medline Rows With NULL issns Will Point To This, 36, 25
- 2006, PNAS, 103, 12115, 10.1073/pnas.0605127103 · DOI
- 2008, ISME J, 2, 265, 10.1038/ismej.2008.5 · DOI
- Lozupone, 2008, FEMS microbiology reviews, 32, 557, 10.1111/j.1574-6976.2008.00111.x · DOI
- An, 2006, International Journal of Systematic and Evolutionary Microbiology, 56, 443, 10.1099/ijs.0.63942-0 · DOI
- 2005, Bioinformatics, 21, 2309, 10.1093/bioinformatics/bti346 · DOI
- Gil, 2008, Omics : a journal of integrative biology, 12, 123, 10.1089/omi.2008.0015 · DOI
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Metadata
- Authors
- Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., Kulam-Syed-Mohideen, A. S., McGarrell, D. M., Marsh, T., Garrity, G. M., & Tiedje, J. M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-01-01
- Volume
- 37
- Issue
- Database
- Pages
- D141-D145
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2155066423
- Cited by
- 4,762
- References
- 0
- FWCI
- 84.99
- Type
- journal article
- Language
- en
- Open access
- gold
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- Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., Kulam-Syed-Mohideen, A. S., McGarrell, D. M., Marsh, T., Garrity, G. M., & Tiedje, J. M. (2009). The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Research. https://doi.org/10.1093/nar/gkn879
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