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TaxCollector: Modifying Current 16S rRNA Databases for the Rapid Classification at Six Taxonomic Levels
Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 1052 Museum Road, Gainesville, FL 32611-0700, USA
* Author to whom correspondence should be addressed.
Received: 16 June 2010; in revised form: 14 July 2010 / Accepted: 19 July 2010 / Published: 21 July 2010
Abstract: The high level of conservation of 16S ribosomal RNA gene (16S rRNA) in all Prokaryotes makes this gene an ideal tool for the rapid identification and classification of these microorganisms. Databases such as the Ribosomal Database Project II (RDP-II) and the Greengenes Project offer access to sets of ribosomal RNA sequence databases useful in identification of microbes in a culture-independent analysis of microbial communities. However, these databases do not contain all of the taxonomic levels attached to the published names of the bacterial and archaeal sequences. TaxCollector is a set of scripts developed in Python language that attaches taxonomic information to all 16S rRNA sequences in the RDP-II and Greengenes databases. These modified databases are referred to as TaxCollector databases, which when used in conjunction with BLAST allow for rapid classification of sequences from any environmental or clinical source at six different taxonomic levels, from domain to species. The TaxCollector database prepared from the RDP-II database is an important component of a new 16S rRNA pipeline called PANGEA. The usefulness of TaxCollector databases is demonstrated with two very different datasets obtained using samples from a clinical setting and an agricultural soil. The six TaxCollector scripts are freely available on http://taxcollector.sourceforge.net and on http://www.microgator.org.
Keywords: 16S rRNA gene; microbial diversity; taxonomy
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Giongo, A.; Davis-Richardson, A.G.; Crabb, D.B.; Triplett, E.W. TaxCollector: Modifying Current 16S rRNA Databases for the Rapid Classification at Six Taxonomic Levels. Diversity 2010, 2, 1015-1025.
Giongo A, Davis-Richardson AG, Crabb DB, Triplett EW. TaxCollector: Modifying Current 16S rRNA Databases for the Rapid Classification at Six Taxonomic Levels. Diversity. 2010; 2(7):1015-1025.
Giongo, Adriana; Davis-Richardson, Austin G.; Crabb, David B.; Triplett, Eric W. 2010. "TaxCollector: Modifying Current 16S rRNA Databases for the Rapid Classification at Six Taxonomic Levels." Diversity 2, no. 7: 1015-1025.