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

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

Published In Nucleic Acids Res, (2009 Jan)

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/.

PubMed ID: 19004872

MeSH Terms: Computer Graphics; Databases, Nucleic Acid*; Internet; RNA, Archaeal/chemistry*; RNA, Archaeal/classification; RNA, Bacterial/chemistry*; RNA, Bacterial/classification; RNA, Ribosomal/chemistry*; RNA, Ribosomal/classification; Sequence Alignment; Sequence Analysis, RNA*; Software