The Ribosomal Database Project: improved alignments and new tools for rRNA analysis.
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/.
Cole
J R
JR
Center for Microbial Ecology and Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA. colej@msu.edu
Wang
Q
Q
Cardenas
E
E
Fish
J
J
Chai
B
B
Farris
R J
RJ
Kulam-Syed-Mohideen
A S
AS
McGarrell
D M
DM
Marsh
T
T
Garrity
G M
GM
Tiedje
J M
JM
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
D019642:RNA, Archaeal; D012329:RNA, Bacterial; D012335:RNA, Ribosomal