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RNAmmer: consistent and rapid annotation of ribosomal RNA genes
Open accessAbstract
The publication of a complete genome sequence is usually accompanied by annotations of its genes. In contrast to protein coding genes, genes for ribosomal RNA (rRNA) are often poorly or inconsistently annotated. This makes comparative studies based on rRNA genes difficult. We have therefore created computational predictors for the major rRNA species from all kingdoms of life and compiled them into a program called RNAmmer. The program uses hidden Markov models trained on data from the 5S ribosomal RNA database and the European ribosomal RNA database project. A pre-screening step makes the method fast with little loss of sensitivity, enabling the analysis of a complete bacterial genome in less than a minute. Results from running RNAmmer on a large set of genomes indicate that the location of rRNAs can be predicted with a very high level of accuracy. Novel, unannotated rRNAs are also predicted in many genomes. The software as well as the genome analysis results are available at the CBS web server.
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Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
Environmental genome shotgun sequencing of the sargasso sea
Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., et al. (2004) · Science · doi:10.1126/science.1093857 · Cited by 4,376
Structure of the 30S ribosomal subunit
Wimberly, B. T., Brodersen, D. E., Clemons, W. M., Morgan-Warren, R. J., Carter, A. P., Vonrhein, C., Hartsch, T., & Ramakrishnan, V. (2000) · Nature · doi:10.1038/35030006 · Cited by 2,035
Crystal structure of the ribosome at 5.5 Å resolution
Yusupov, M. M., Yusupova, G. Z., Baucom, A., Lieberman, K., Earnest, T. N., Cate, J. H. D., & Noller, H. F. (2001) · Science · doi:10.1126/science.1060089 · Cited by 1,944
Structure of Functionally Activated Small Ribosomal Subunit at 3.3 Å Resolution
Schluenzen, F., Tocilj, A., Zarivach, R., Harms, J., Gluehmann, M., Janell, D., Bashan, A., Bartels, H., Agmon, I., Franceschi, F., et al. (2000) · Cell · doi:10.1016/s0092-8674(00)00084-2 · Cited by 979
Research works printed but not linked: 21
- Freyhult, 2007, Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA, Genome Res., 17, 117, 10.1101/gr.5890907 · DOI
- Pedersen, 2000, A DNA structural atlas for Escherichia coli, J. Mol. Biol, 299, 907, 10.1006/jmbi.2000.3787 · DOI · Paper page
- Nissen, 2000, The structural basis of ribosome activity in peptide bond synthesis, Science, 289, 920, 10.1126/science.289.5481.920 · DOI · Paper page
- Srivastava, 1991, Structure and organization of ribosomal DNA, Biochimie, 73, 631, 10.1016/0300-9084(91)90042-Y · DOI
- Acinas, 2004, Divergence and redundancy of 16s rRNA sequences in genomes with multiple rrn operons, J Bacteriol, 186, 2629, 10.1128/JB.186.9.2629-2635.2004 · DOI · Paper page
- Jackson, 2002, Distribution of rRNA introns in the three-dimensional structure of the ribosome, J Mol Biol, 323, 35, 10.1016/S0022-2836(02)00895-1 · DOI
- Evguenieva-Hackenberg, 2005, Bacterial ribosomal RNA in pieces, Mol Microbiol, 57, 318, 10.1111/j.1365-2958.2005.04662.x · DOI · Paper page
- Wuyts, 2004, The European ribosomal RNA database, Nucleic Acids Res, 32, 10.1093/nar/gkh065 · DOI · Paper page
- Szymanski, 2002, 5s Ribosomal RNA database, Nucleic Acids Res, 30, 176, 10.1093/nar/30.1.176 · DOI · Paper page
- Hobohm, 1992, Selection of representative protein data sets, Protein Sci., 1, 409, 10.1002/pro.5560010313 · DOI · Paper page
- Eddy, 1998, Profile hidden markov models, Bioinformatics, 14, 755, 10.1093/bioinformatics/14.9.755 · DOI · Paper page
- Henikoff, 1994, Position-based sequence weights, J. Mol. Biol., 243, 574, 10.1016/0022-2836(94)90032-9 · DOI · Paper page
- Griffiths-Jones, 2005, Rfam: annotating non-coding RNAs in complete genomes, Nucleic Acids Res, 33
- Griffiths-Jones, 2003, Rfam: an RNA family database, Nucleic Acids Res, 31, 439, 10.1093/nar/gkg006 · DOI · Paper page
- Rognes, 2001, ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches, Nucleic Acids Res, 29, 1647, 10.1093/nar/29.7.1647 · DOI
- Pearson, 1988, Improved tools for biological sequence comparison, Proc. Natl. Acad. Sci. USA, 85, 2444, 10.1073/pnas.85.8.2444 · DOI · Paper page
- Durbin, 2000, Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
- Lowe, 1997, tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence, Nucleic Acids Res, 25, 955, 10.1093/nar/25.5.0955 · DOI · Paper page
- Eddy, 2002, A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure, 18
- Weinberg, 2006, Sequence-based heuristics for faster annotation of non-coding RNA families, Bioinformatics, 22, 10.1093/bioinformatics/bti743 · DOI
- Weinberg, 2004, RECOMB 04: Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, 243, 10.1145/974614.974647 · DOI
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The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1219 · Cited by 33,055
Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice
Ridaura, V. K., Faith, J. J., Rey, F. E., Cheng, J., Duncan, A. E., Kau, A. L., Griffin, N. W., Lombard, V., Henrissat, B., Bain, J. R., et al. (2013) · Science · doi:10.1126/science.1241214 · Cited by 3,788
Complex archaea that bridge the gap between prokaryotes and eukaryotes
Spang, A., Saw, J. H., Jørgensen, S. L., Zaremba-Niedzwiedzka, K., Martijn, J., Lind, A. E., van Eijk, R., Schleper, C., Guy, L., & Ettema, T. J. G. (2015) · Nature · doi:10.1038/nature14447 · Cited by 1,324
IMG: the integrated microbial genomes database and comparative analysis system
Markowitz, V. M., Chen, I.-M. A., Palaniappan, K., Chu, K., Szeto, E., Grechkin, Y., Ratner, A., Jacob, B., Huang, J., Williams, P., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1044 · Cited by 1,311
Individual intestinal symbionts induce a distinct population of RORγ + regulatory T cells
Sefik, E., Geva-Zatorsky, N., Oh, S., Konnikova, L., Zemmour, D., McGuire, A. M., Burzyn, D., Ortiz-Lopez, A., Lobera, M., Yang, J., et al. (2015) · Science · doi:10.1126/science.aaa9420 · Cited by 879
Metadata
- Authors
- Lagesen, K., Hallin, P., Rødland, E. A., Stærfeldt, H.-H., Rognes, T., & Ussery, D. W.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-04-22
- Volume
- 35
- Issue
- 9
- Pages
- 3100-3108
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2045843097
- Cited by
- 6,112
- References
- 5
- FWCI
- 10.66
- Type
- journal article
- Language
- en
- Open access
- gold
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