Ribosomal Database Project: Release 10

RDP Resource Download Area

Please take a moment to review our License Agreement before downloading any data from our site.

Page Contents:

• Current release alignments
• Posters and Presentations
• Surveys
• User Submitted Resources

 

Release 10 Alignment:

These files reflect the contents of the current RDP Release 10 data. Please see the release notes for more information.

A histogram of the number of RDP sequences spanning each base position is available.

Details of sequence quality check by RDP is available.

These files were compressed using bzip2. Common decompression programs should be able to decompress these files. Mac OS X and Linux should have built in support for bzip2. Windows users may consider the free and open source decompression program 7-Zip.

The aligned files will unzip to 2-30 GB in size. Lack of available disk space is the most commonly encountered problem when decompressing these files.

 

Surveys:

RDP Survey Results

 

Posters and Presentations:

These posters were presented by the RDP at the International Society for Microbial Ecology Biennial Symposia.

2008 ISME Poster (8MB pdf)
2006 ISME poster (1.2MB pdf)

These posters were presented by the RDP at the American Society for Microbiology annual meetings.

Slideshow Pyrosequencing-Enabled Large Scale, Rapid and Parallel Analysis of Microbial Community Structure and Functions (ASM Session 203/N, May 19, 2009)
2009 RDP Poster (13MB pdf)
2008 RDP Poster (8MB pdf)
2008 Pyrosequencing Pipeline Poster (8.6MB pdf)
2007 Poster (5.7MB pdf)
2006 Poster (4.3MB pdf)
2005 Poster (3MB pdf)
2004 Poster (1.2MB pdf)
2003 Poster (1.1MB pdf)
2002 Poster (1.6MB pdf)
2001 Poster (1.2MB pdf)
2000 Poster (220KB pdf), Sequence Space supplement (3.2MB pdf), Backbone Tree supplement (62KB pdf)

 

User Submitted Resources:

The following have been submitted by RDP-II Users. Please refer to the original publication for more information.

GenBank accession mappings for sequences used in Kuske's 2007 AEM paper

Click here to download GenBank accession mappings for the 26 groups discussed in Kuske, S. and S. Barns (2007). Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum. Appl. Environ. Microbiol. 73(9):3113-3116. PubMed. To retrieve the sequences from RDP, upload the accessions into your seqCart.

Universally Conserved Genes

Santos, S. R. and Howard Ochman. Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environmental Microbiology. 2004. Jul(6)7:754-9. [PubMed 15186354]

Scott Santos and Howard Ochman (University of Arizona, Tucson) have graciously made the sequence data from their paper available for distribution by the Ribosomal Database Project along with additional genes and sequences developed since publication. Also see RDP's Functional Gene Pipeline and Repository.

Right Click to Download Files
fusA	ileS	lepA	leuS	pyrG	recA	recG	rplB	rpoB
DNA fasta	DNA fasta	DNA fasta	DNA fasta	DNA fasta	DNA fasta	DNA fasta	DNA fasta	DNA fasta
DNA nexus	DNA nexus	DNA nexus	DNA nexus	DNA nexus	DNA nexus	DNA nexus	DNA nexus	DNA nexus
Protein fasta	Protein fasta	Protein fasta	Protein fasta	Protein fasta	Protein fasta	Protein fasta	Protein fasta	Protein fasta
Protein nexus	Protein nexus	Protein nexus	Protein nexus	Protein nexus	Protein nexus	Protein nexus	Protein nexus	Protein nexus

Philip Hugenholtz's 16S rRNA ARB Database

Hugenholtz, Philip (January 2002) Exploring prokaryotic diversity in the genomic era. Genome Biology 3(2):reviews0003.1-0003.8
[ http://genomebiology.com/2002/3/2/reviews/0003 (Access to article requires subscription) ]
Release Notes  -  ARB File (6.3MB)

Improved Protocol for T-RFLP by Capillary Electrophoresis

A protocol for improved T-RFLP by capillary electrophoresis, which includes a sample, PCR protocol information, references and suggested readings. From V. Grüntzig, B. Stres, H. L. Ayala del Río, and J. M. Tiedje of MSU's Center for Microbial Ecology.

 

Questions/comments: rdpstaff@msu.edu

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