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RDP Resource Download Area


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

Page Contents:

 

RDP Tools Repository -- Run RDP Tools Locally

Install RDP tools to your local computer, available from GitHub https://github.com/rdpstaff
(RDP Aligners, Classifier, Clustering, FrameBot, GFClassify, Initial Process, KmerFilter, ProbeMatch, ReadSeq, SequenceMatch, SOAP-examples, Xander-HMMgs)

For the pre-compiled RDP Classifier and FrameBot command line tools and training data, visit Sourceforge:
http://sourceforge.net/projects/rdp-classifier/files/
and http://sourceforge.net/projects/rdpframebot/

The current training files and pre-built models for Infernal 1.1 are available here RDP 11 Aligner.

The RDP Paired-end Reads Assembler used in the publication Cole et al., 2014 is available here RDP Paired-end Reads Assembler. This version provides built-in quality filtering and more command-line options using the RDP algorithm than the one available on the original Pandaseq GitHub repository.
Note: if you run the Assembler program downloaded from the original Pandaseq GitHub repository, specify command-line option "-A rdp_mle" to use RDP's algorithm, and option "-C min_readqscore:25" to filter any assembled reads with Read Q score less than 25.

The most current RDP Classifier training sets (including 16S rRNA, fungal 28S, Warcup fungal ITS and UNITE fungal ITS) are available. The Fungal ITS Warcup V2 release notes is released in June 2016.

 

Release Alignment:

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

Gene Aligned FASTA Unaligned Coverage Chart
Bacteria 16S Aligned Fasta, Genbank Excel
Archaea 16S Aligned Fasta, Genbank Excel
Fungal 28S Aligned Fasta, Genbank Excel

Details of sequence quality check by RDP is available.

These files were compressed using gzip. Common decompression programs should be able to decompress these files. Mac OS X and Linux should have built in support for gzip. 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.

 

Help Topics:

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RDP's New Workflow Tutorials
Soap web services
RDP quality control steps
Xander: Gene-targeted Metagenomic Assembler

 

Surveys:

RDP Survey Results
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Posters and Presentations:

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

2012 ISME Poster (3.7MB pdf)
2010 ISME RDP Poster (4.4MB pdf)
2010 ISME FunGene Poster (5.3MB pdf)
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.

2015 RDP Poster (3MB pdf)
2015 Xander Poster (3MB pdf)
2014 RDP ppt for ASM Conference for Undergraduate Educators (3.4MB pdf)
2014 RDP Poster (2.7MB pdf)
2013 RDP Poster (2.7MB pdf)
2012 RDP Poster (15MB pdf)
2012 RDP Fungene Poster (15MB pdf)
2011 RDP Poster (15MB pdf)
2010 RDP Poster (17MB pdf)
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)

These posters were presented by the RDP at the Mycological Society of America Annual Symposia.

2014 MSA Poster (3.9MB pdf)

 

User Submitted Resources:

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The following have been submitted by RDP 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)


 

Questions/comments: rdpstaff@msu.edu
Creative Commons License: Attribution-ShareAlike

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