Ribosomal Database Project: Release 10

Ribosomal Database Project Release 10 (RDP) Notes

RDP 10.5 (Release 10, Update 5) consists of 706,103 aligned and annotated 16S rRNA sequences.

Please note the RDP License Agreement and how to cite services from this site.

Page Contents:

• Changes from RDP9 Releases
• Changes from RDP8.1 and Earlier Versions
• Notes and Clarifications About RDP
• References
• RDP Release 10 Issues
• Update History

 

Changes from RDP Release 9

RDP10 provides two significant enhancements over RDP9:

Archaea Sequences

This release of the RDP includes Archaea sequences. Aligned and annotated public Archaea sequence data is available from our Hierarchy Browser, the RDP Classifier and Seqmatch can be used to classify and match Archaea sequences, and user's private sequence data can be uploaded and aligned against RDP's Archaea alignment model.

Improved Alignment Strategy

RDP Bacterial and Archaeal alignments are now produced using Infernal (1), a secondary-structure based aligner that provides better support for short partial sequences and handles certain sequencing artifacts in a more intuitive manner. The aligner is trained on sets of high quality hand-aligned sequences and incorporates the conserved Bacterial and Archaeal secondary structure models of Gutell and co-workers (2).

 

Changes From RDP8.1 and Earlier Versions

Taxonomy

Since RDP Release 9, all tools use a new RDP Hierarchy which differs significantly from the Release 8.1 and earlier Hierarchy. The RDP Hierarchy is now based on the new phylogenetically consistent higher-order bacterial taxonomy proposed by Garrity et. al (3), with additional major rearrangements that have been proposed for the Firmicutes (8) and Cyanobacteria (7). It also includes published informal classifications for well-defined lineage with few cultivated members, such as Acidobacteria, Verrucomicrobia and OP11 (4, 5, 6). Additional information for the classification of chloroplast, Korarchaeota, and Nanoarchaeum were taken from the NCBI taxonomy (9). Sequences are placed in the Hierarchy using the RDP Classifier.

Some tools also allow the user to view data in a taxonomy as classified by NCBI.

Data Updates

Release 10 is kept up-to-date by syncing its sequence data with the major sequence repositories about once every month. New public sequences are added to the RDP, deleted sequences are removed, and annotation is updated with every update. Each update of the RDP is given a specific update number, such as RDP 10.1 (RDP 10, update 1), RDP 10.2, etc.

Quality Checking for Public Sequence Data

Since RDP Release 9, public data added to the RDP is labeled as being either "good" or "suspect" in quality. Suspected low quality sequences may be chimeric or have other sequencing related issues. Quality checking is performed using a combination of Pintail and the RDP Seqmatch. More information is available about RDP's quality checking algorithm.

 

Notes and Clarifications about RDP Release 10

Alignments

RDP Bacterial and Archaeal alignments are created from separate alignment models. This means a user cannot download an aligned file containing both Archaea and Bacteria sequences, or run an analysis program that requires aligned data (eg. TreeBuilder) on a mixed set of Bacteria and Archaea sequences. However, each alignment includes one cross-aligned sequence (either E.Coli or Methanocaldococcus jannaschii) that can be used as an outgroup if needed for trees, etc.

Using separate alignment models for Archaea and Bacteria maximizes the number of comparable base positions within each alignment, resulting in more data or meaning being encoded in the alignment. However, if you would still find a "combined" alignment with a reduced number of comparable alignment positions useful, please contact us. We are considering adding this as an option at some future point, but are unsure of its usefulness to our users.

myRDP, RDP10 and RDP9

myRDP account information--including usernames, passwords, and uploaded sequence data--is shared between the RDP10 and RDP9 websites. All myRDP user sequences were realigned using the RDP10 alignment model. Log into the RDP9 website to use the old RDP9 alignment, and log into the RDP10 website for the new Release 10 alignment models. Sequences uploaded to RDP10 to be aligned using our Archaea aligner will show up under RDP9's myRDP site as unaligned.

 

References

1.Nawrocki , E. P. and S. R. Eddy. 2007. Query-Dependent Banding (QDB) for Faster RNA Similarity Searches. PLoS Comput. Biol., 3:e56. [PubMed]

2. Cannone, J.J., Subramanian, S., Schnare, M.N., Collet, J.R., D'Souza, L.M., Du, Y., Feng, B., Lin, N., Madabusi, L.V., Muller, K.M., Pande, N., Shang, Z., Yu, N., and Gutell, R.R. (2002) The Comparative RNA Web (CRW) Site: An Online Database of Comparative Sequence and Structure Information for Ribosomal, Intron, and other RNAs. BioMed Central Bioinformatics., 3,2. [PubMed]

3. Garrity, G.M., Lilburn, T.G., Cole, J.R., Harrison, S.H., Euzeby, J., and Tindall, B.J. (2007) The Taxonomic Outline of Bacteria and Archaea. TOBA Release 7.7, March 2007. Michigan State University Board of Trustees. [http://www.taxonomicoutline.org/]

4. Barns, S. M, E. C. Cain, L. Sommerville and C. R. Kuske. 2007. Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum. Appl Environ Microbiol. 73(9):3113-6. [PubMed]

5. Sangwan, P, X. Chen, P. Hugenholtz and P. H. Janssen. 2004. Chthoniobacter flavus gen. nov., sp. nov., the first pure-culture representative of subdivision two, Spartobacteria classis nov., of the phylum Verrucomicrobia. Appl Environ Microbiol. 70(10):5875-81. [PubMed]

6. Harris, J. K, S. T. Kelley and N. R. Pace. 2004. New Perspective on Uncultured Bacterial Phylogenetic Division OP11. Appl Environ Microbiol. 70(2):845-9. [PubMed]

7. Wilmotte, A. and M. Herdman. 2001. Phylogenetic relationships among the Cyanobacteria based on 16S rRNA sequences. Bergey's Manual of Systematic Bacteriology. 2nd Ed.. Volume 1, p. 487-493. Springer-Verlag, New York.

8. Ludwig, W., K.-H. Schleifer and W. B. Whitman. 2008. Revised Road Map to the Phylum Firmicutes. Bergey's Manual of Systematic Bacteriology. Volume 3. Springer-Verlag, New York.

9. Wheeler DL, C. Chappey, A.E. Lash, D.D. Leipe, T.L. Madden, G.D. Schuler, T.A. Tatusova, B.A. Rapp. 2000. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 28(1):10-14.

 

RDP Release 10 Issues

The following are known issues with the RDP Release 10 site:

Video Tutorials

The video tutorials may not mention the multiple alignment models available.

 

Update History

10/30/2008	RDP 10.5: 15,954 new sequences added (706,103 total).
10/01/2008	RDP 10.4: 13,092 new sequences added (690,149 total).
09/04/2008	RDP 10.3: 53,883 new sequences added (677,057 total).
08/01/2008	RDP 10.2: 72,808 new sequences added (623,174 total). Probematch can now restrict searches by e.coli position or kingdom. Class Assignment Generator has been updated to also include Archaea sequences in student assignments. Release 10 is no longer beta, and replaces Release 9 as the latest RDP Release.
05/22/2008	RDP 10.1: Initial preview/beta release with 550,366 sequences.

 

Questions/comments: rdpstaff@msu.edu

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