title: The Ribosomal Database Project: improved alignments and new tools for rRNA analysis.
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/.
authors.affiliation: Center for Microbial Ecology and Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA. colej@msu.edu
authors.forename: J R
authors.initials: JR
authors.lastname: Cole
authors.forename: Q
authors.initials: Q
authors.lastname: Wang
authors.forename: E
authors.initials: E
authors.lastname: Cardenas
authors.forename: J
authors.initials: J
authors.lastname: Fish
authors.forename: B
authors.initials: B
authors.lastname: Chai
authors.forename: R J
authors.initials: RJ
authors.lastname: Farris
authors.forename: A S
authors.initials: AS
authors.lastname: Kulam-Syed-Mohideen
authors.forename: D M
authors.initials: DM
authors.lastname: McGarrell
authors.forename: T
authors.initials: T
authors.lastname: Marsh
authors.forename: G M
authors.initials: GM
authors.lastname: Garrity
authors.forename: J M
authors.initials: JM
authors.lastname: Tiedje
mesh_terms: D003196:Computer Graphics; D030561:Databases, Nucleic Acid; D020407:Internet; D019642:RNA, Archaeal / Q000737:chemistry* / Q000145:classification; D012329:RNA, Bacterial / Q000737:chemistry* / Q000145:classification; D012335:RNA, Ribosomal / Q000737:chemistry* / Q000145:classification; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D019642:RNA, Archaeal; D012329:RNA, Bacterial; D012335:RNA, Ribosomal