The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

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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·Nucleic Acids Research

DOI 10.1093/nar/gkn879

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Abstract

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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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

Items 101–144 of 144

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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
DOI: 10.1093/nar/gkn879
OpenAlex: W2155066423
Cited by: 4,762
References: 0
FWCI: 84.99
Type: journal article
Language: en
Open access: gold
Licence: creativecommons.org/licenses/by-nc/2.0/uk/ (vor, 2833 d)

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The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

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