Ribosomal Database Project (RDP-II)

Other names: RDP, Ribosomal Database Project, Ribosomal Database Project (RDP), rdp

The Ribosomal Database Project - II (RDP-II)(1) provides 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. Currently available on the RDP-II website as a beta release, 9.0 provides over 50,000 annotated (eu)bacterial sequences aligned with a secondary-structure based alignment algorithm (2). We feel these alignments are, for most purposes, of equal utility to hand-alignments, but without any unintended bias or other potential hand-alignment artifacts. At least monthly updates are scheduled for this new alignment, and similar alignments will be released for archaeal, eukaryotic, and mitochondrial small-subunit rRNA sequences. This new alignment can be displayed using either the taxonomy assigned by NCBI or in a schema closely matching the taxonomy proposed by Garrity et al. (3). Data subsets are available for sequences of length 1200 or greater and for sequences from type material. Annotation goals include up-to-date name, strain and culture deposit information, sequence length and quality information, references, and, in collaboration with Bergey's Trust (3), type status. In order to provide a phylogenetic context for the data, RDP-II makes available over 100 trees that span the phylogenetic breadth of life. Web based research tools are provided for comparing user submitted sequences to the RDP-II database (Sequence Match), aligning user sequences against the nearest RDP sequence (Sequence Aligner), examining probe and primer specificity (Probe Match), testing for chimeric sequences (Chimera Check), generating a distance matrix (Similarity Matrix), analyzing T-RFLP data (T-RFLP and TAP-TRFLP), a java-based phylogenetic tree browser (Sub Trees), a sequence search and selection tool (Hierarchy Browser) and a phylogenetic tree building and visualization tool (Phylip Interface). The latter tool has been enhanced to allow a choice of either the Phylip neighbor-joining (4) or Weighbor weighted neighbor-joining (5) programs for tree construction. In addition, the web-site includes an interactive tutorial to guide users through the basics of rRNA sequence analysis. This tutorial is suitable both for the researcher new to rRNA based phylogenetic analysis and as a teaching module for upper-level undergraduate and graduate classes. The RDP-II email address for questions or comments is [email protected]

Webpage:
http://rdp.cme.msu.edu/

Licence:
Name: CC
URL: https://creativecommons.org/licenses/by-sa/3.0/

Publications:

Tags:

rna sequence genomics taxonomy and identification archaea sequences bacteria sequences dna microbiome phylogenetic trees protein biosynthesis rrna sequences phylogeny model organisms sequence analysis transcription factors and regulatory sites

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