title: The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy.
abstract: The Ribosomal Database Project-II (RDP-II) pro-vides data, tools and services related to ribosomal RNA sequences to the research community. Through its website (http://rdp.cme.msu.edu), RDP-II offers aligned and annotated rRNA sequence data, analysis services, and phylogenetic inferences (trees) derived from these data. RDP-II release 8.1 contains 16 277 prokaryotic, 5201 eukaryotic, and 1503 mitochondrial small subunit rRNA sequences in aligned and annotated format. The current public beta release of 9.0 debuts a new regularly updated alignment of over 50 000 annotated (eu)bacterial sequences. New analysis services include a sequence search and selection tool (Hierarchy Browser) and a phylogenetic tree building and visualization tool (Phylip Interface). A new interactive tutorial guides users through the basics of rRNA sequence analysis. Other services include probe checking, phylogenetic placement of user sequences, screening of users' sequences for chimeric rRNA sequences, automated alignment, production of similarity matrices, and services to plan and analyze terminal restriction fragment polymorphism (T-RFLP) experiments. The RDP-II email address for questions or comments is rdpstaff@msu.edu.
authors.affiliation: Center for Microbial Ecology, 2225A Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA. rdpstaff@msu.edu
authors.forename: J R
authors.initials: JR
authors.lastname: Cole
authors.forename: B
authors.initials: B
authors.lastname: Chai
authors.forename: T L
authors.initials: TL
authors.lastname: Marsh
authors.forename: R J
authors.initials: RJ
authors.lastname: Farris
authors.forename: Q
authors.initials: Q
authors.lastname: Wang
authors.forename: S A
authors.initials: SA
authors.lastname: Kulam
authors.forename: S
authors.initials: S
authors.lastname: Chandra
authors.forename: D M
authors.initials: DM
authors.lastname: McGarrell
authors.forename: T M
authors.initials: TM
authors.lastname: Schmidt
authors.forename: G M
authors.initials: GM
authors.lastname: Garrity
authors.forename: J M
authors.initials: JM
authors.lastname: Tiedje
mesh_terms: D000818:Animals; D001105:Archaea / Q000145:classification* / Q000235:genetics; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D030561:Databases, Nucleic Acid; D005057:Eukaryotic Cells / Q000145:classification; D010802:Phylogeny; D011387:Prokaryotic Cells / Q000145:classification; 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