The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis

Nucleic Acids Research

Volumn 37, Issue SUPPL. 1, 2009, Pages

  Cole, J R ^a   Wang, Q ^a   Cardenas, E ^a   Fish, J ^b   Chai, B ^a   Farris, R J ^a   Kulam Syed Mohideen, A S ^a   McGarrell, D M ^a   Marsh, T ^a,b   Garrity, G M ^b   Tiedje, J M ^a,b  

^a MICHIGAN STATE UNIVERSITY   (United States)

^b NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME RNA;

ARCHAEBACTERIUM; ARTICLE; AUTOMATION; BACTERIUM; COMPUTER INTERFACE; INFORMATION PROCESSING; NONHUMAN; NUCLEIC ACID DATABASE; NUCLEIC ACID STRUCTURE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA ANALYSIS; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ALIGNMENT; TAXONOMY;

COMPUTER GRAPHICS; DATABASES, NUCLEIC ACID; INTERNET; RNA, ARCHAEAL; RNA, BACTERIAL; RNA, RIBOSOMAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; SOFTWARE;

ARCHAEA; BACTERIA (MICROORGANISMS);

EID: 58149200948     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn879     Document Type: Article

References (23)

1. Cole,J.R., Chai,B., Farris,R.J., Wang,Q., Kulam-Syed-Mohideen,A.S., McGarrell,D.M., Bandela,A.M., Cardenas,E., Garrity,G.M., Tiedje,J.M. et al. (2007) The ribosomal database project (RDP-II): Introducing myRDP space and quality controlled public data. Nucleic Acids Res. 35, D169-D172. (doi: 10.1093/nar/gkl889)
2. Ashelford,K.E., Chuzhanova,N.A., Fry,J.C., Jones,A.J. and Weightman,A.J. (2005) At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl. Environ. Microbiol., 71, 7724-7736.
3. Nawrocki,E.P. and Eddy,S.R. (2007) Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Comput. Biol., 3, e56.
4. Griffiths-Jones,S., Moxon,S., Marshall,M., Khanna,A., Eddy,S.R. and Bateman,A. (2005) Rfam: Annotating non-coding RNAs in complete genomes. Nucleic Acids Res., 33, D121-D124.
5. Brown,M.P.S. (2000) Small subunit ribosomal RNA modeling using stochastic context-free grammar. In Bourne,P., Gribskov,M., Altman,R., Jensen,N., Hope,D., Lengauer,T., Mitchell,J., Schee.,E., Smith,C., Strande,S., et al. (eds.) Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology (ISMB 2000), San Diego, CA, pp. 57-66.
6. Ashelford,K.E., Chuzhanova,N.A., Fry,J.C., Jones,A.J. and Weightman,A.J. (2006) New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl. Environ. Microbiol., 72 5734-5741.
7. Lagesen,K., Hallin,P., Rødland,E.A., Staerfeldt,H.H., Rognes,T. and Ussery,D.W. (2007) RNAmmer: Consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res., 35, 3100-3108.
8. Cannone,J.J., Subramanian,S., Schnare,M.N., Collett,J.R., D'Souza,L.M., Du,Y., Feng,B., Lin,N., Madabusi,L.V., Muller,K.M. et al. (2002) The comparative RNA web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics, 3, 2.
9. 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. Michigan State University Board of Trustees, MI, USA.
10. Ludwig,W., Schleifer,K.-H. and Whitman,W.B. (2008) Revised Road Map to the Phylum Firmicutes. Bergey's Manual of Systematic Bacteriology, Vol. 3, Springer-Verlag, New York.
11. Wilmotte,A. and Herdman,M. (2001) Phylogenetic relationships among the Cyanobacteria based on 16S rRNA sequences. In Garrity,G.M., Boone,D.R. and Castenholz,R.W. (eds) Bergey's Manual of Systematic Bacteriology, Vol. 1, 2nd edn. Springer-Verlag, New York, pp. 487-493.
12. Barns,S.M., Cain,E.C., Sommerville,L. and Kuske,C.R. (2007) Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum. Appl. Environ. Microbiol., 73, 3113-3116.
13. Sangwan,P., Chen,X., Hugenholtz,P. and Janssen,P.H. (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, 5875-5881.
14. Harris,J.K., Kelley,S.T. and Pace,N.R. (2004) New perspective on uncultured bacterial phylogenetic division OP11. Appl. Environ. Microbiol., 70, 845-849.
15. Wang,Q., Garrity,G.M., Tiedje,J.M. and Cole,J.R. (2007) Naive bayesian classi.er for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol., 73, 5261-5267.
16. Benson,D.A., Karsch-Mizrachi,I., Lipman,D.J., Ostell,J. and Wheeler,D.L. (2007) Genbank. Nucleic Acids Res., 36, 25-30.
17. Sogin,M.L., Morrison,H.G., Huber,J.A., Welch,D.M., Huse,S.M., Neal,P.R., Arrieta,J.M. and Herndl,G.J. (2006) Microbial diversity in the deep sea and the underexplored 'rare biosphere'. Proc. Natl Acad. Sci. USA, 103, 12115-12120.
18. Schloss,P.D. (2008) Evaluating di.erent approaches that test whether microbial communities have the same structure. ISME J., 2, 265-275.
19. Lozupone,C.A. and Knight,R. (2008) Species divergence and the measurement of microbial diversity. FEMS Microbiol. Rev., 32 (4), 557-578.
20. Liu,Z., Desantis,T.Z., Andersen,G.L. and Knight,R. (2008) Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Res. [Epub Aug 22, doi:10.1093/nar/ gkn491]
21. An,D.S., Im,W.T., Yang,H.C. and Lee,S.T. (2006) Shinella granuli gen. nov., sp. nov., and proposal of the reclassification of Zoogloea ramigera ATCC 19623 as Shinella zoogloeoides sp. nov. Int. J. Syst. Evol. Microbiol., 56, 443-448.
22. Garrity,G.M. and Lilburn,T.G. (2005) Self-organizing and selfcorrecting classifications of biological data. Bioinformatics, 21, 2309-2314.
23. Van Brabant,B., Gray,T., Verslyppe,B., Kyrpides,N., Dietrich,K., Glöckner,F.O., Cole,J., Farris,R., Schriml,L.M., De Vos,P. et al. (2008) Laying the foundation for a Genomic Rosetta Stone: Creating information hubs through the use of consensus identifiers. OMICS, 12(2), 123-127. (doi:10.1089/omi.2008.0020)