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RDP 11 Release Notes


RDP Release 11 consists of 2,809,406 16S and 62,860 Fungal 28S aligned and annotated rRNA sequences.

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

Page Contents:

 

Changes from RDP Release 9

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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

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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.

Major rearrangements for Classifier training set No. 9 include the following:

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.

10. Tamaki,H., Tanaka,Y., Matsuzawa,H., Muramatsu,M., Meng,X.Y., Hanada,S., Mori,K. and Kamagata,Y. 2011. Armatimonas rosea gen. nov., sp. nov., of a novel bacterial phylum, Armatimonadetes phyl. nov., formally called the candidate phylum OP10. Int. J. Syst. Evol. Microbiol. 61(PT 6):1442-47. [PubMed]

11. Lee,K.C., Dunfield,P.F., Morgan,X.C., Crowe,M.A., Houghton,K.M., Vyssotski,M., Ryan,J.L., Lagutin,K., McDonald,I.R. and Stott,M.B. 2011. Chthonomonas calidirosea gen. nov., sp. nov., an aerobic, pigmented, thermophilic micro-organism of a novel bacterial class, Chthonomonadetes classis nov., of the newly described phylum Armatimonadetes originally designated candidate division OP10. Int. J. Syst. Evol. Microbiol. 61 (PT 10), 2482-2490. [PubMed]

12. Rainey, F.A., Hollwen, B.J., and Small, A. Genus I. Clostridium Prazmowski 1880, 23. 2008. Bergey's Manual of Systematic Bacteriology. Volume 3, p. 738-741. Springer-Verlag, New York.

 

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

05/14/2013

RDP 10.32: 126,121 new sequences added (2,765,278 total).

12/07/2012

RDP 10.31: 60,255 new sequences added (2,639,157 total).

09/19/2012

RDP 10.30: 259,863 new sequences added (2,578,902 total).

06/01/2012

RDP 10.29: 210,206 new sequences added (2,320,464 total). The hierarchy model used by RDP Classifier has been updated to training set No. 9 with minor rearrangements. The updates include adding new class Negativicutes, order Selenomonadales and family Acidaminococcaceae to phylum Firmicutes, moving family Veillonellaceae to order Selenomonadales. RDP Classifier software package has been updated to version 2.5. Starting from this release, RDP switches to use Uchime with a reference database to detect chimeras.

01/13/2012

RDP 10.28: 189,079 new sequences added (2,110,258 total). The hierarchy model used by RDP Classifier has been updated to training set No. 7. There are 10,046 sequences included in the new training set (19% more than the previous training set No. 6). About 1% public RDP sequences changed phyla. About 4.9% of sequences were classified to greater taxonomic depth in the new release, while about 4.8% were classified with confidence at lesser levels. See more rearrangements details at Taxonomy.

08/09/2011

RDP 10.27: 308,116 new sequences added (1,921,179 total).

06/13/2011

The RDP Fungal LSU Classifier (large subunit rRNA gene) is released, our thanks to Cheryl Kuske and colleagues for providing the hierarchy model and training set.

03/28/2011

RDP 10.26: 67,383 new sequences added (1,613,063 total).

02/17/2011

RDP 10.25: 47,003 new sequences added (1,545,680 total).

01/11/2011

RDP 10.24: 15,661 new sequences added (1,498,677 total).

12/07/2010

RDP 10.23: 64,519 new sequences added (1,483,016 total).

08/30/2010

RDP 10.22: 39,073 new sequences added (1,418,497 total).

07/14/2010

RDP 10.21: 141,461 new sequences added (1,379,424 total).

05/19/2010

RDP 10.20: 0 new sequences added (1,237,963 total). Removed large datasets with only partial 454 sequences.

03/31/2010

RDP 10.19: 38,367 new sequences added (1,396,793 total). Minor updates on the Hierarchy model used by RDP. The hierarchy model used by RDP Classifier is updated to training set No. 6.

01/25/2010

RDP 10.18: 77,329 new sequences added (1,358,426 total). The hierarchy model used by RDP Classifier has been updated to training set No. 5. 101 taxa were removed and 544 taxa were added to the new hierarchy. About 0.9% public RDP sequences changed phyla. About 9.6% of sequences were classified to greater taxonomic depth in the new release, while about 9.1% were classified with confidence at lesser levels.

12/09/2009

RDP 10.17: 46,053 new sequences added (1,281,097 total).

11/10/2009

RDP 10.16: 130,661 new sequences added (1,235,044 total).

10/05/2009

RDP 10.15: 30,308 new sequences added (1,104,383 total).

08/31/2009

RDP 10.14: 24,642 new sequences added (1,074,075 total).

07/28/2009

RDP 10.13: 128,790 new sequences added (1,049,433 total).

06/10/2009

RDP 10.12: 64,302 new sequences added (920,643 total).

05/07/2009

RDP 10.11: 19,527 new sequences added (856,341 total).

04/03/2009

RDP 10.10: 36,655 new sequences added (836,814 total).

03/06/2009

RDP 10.9: 20,656 new sequences added (800,159 total).

02/09/2009

RDP 10.8: 19,666 new sequences added (779,503 total).

01/14/2009

RDP 10.7: 44,200 new sequences added (759,837 total).

12/03/2008

RDP 10.6: 9,534 new sequences added (715,637 total).

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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