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Comparative Study
. 2007;35(9):3100-8.
doi: 10.1093/nar/gkm160. Epub 2007 Apr 22.

RNAmmer: Consistent and Rapid Annotation of Ribosomal RNA Genes

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Free PMC article
Comparative Study

RNAmmer: Consistent and Rapid Annotation of Ribosomal RNA Genes

Karin Lagesen et al. Nucleic Acids Res. .
Free PMC article

Abstract

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.

Figures

Figure 1.
Figure 1.
The graphs show conservation in the alignments as measured by information content: C=∑ifilog2(fi/qi) where i sums over the four nucleotides, fi is the frequency of nucleotide i in the column and qi =1/4 is used as the background frequency. Ambiguous nucleotide symbols were evenly divided between the corresponding fi, gaps between all four nucleotides. The grey line represents the value for each position in the alignment, the black line is a running average over 75 nt around the current position, whereas the white dot indicates the center of the most conserved 75 nt region of the alignment.
Figure 2.
Figure 2.
Deviation of start and stop positions between predicted and annotated RNA is presented as pairs of panels. The number of predictions among the archaea, bacteria and eukaryotes are denoted beneath the panel group heading. The zero position in each panel corresponds to the annotation start or stop position with predicted positions presented relative to these. The yellow dot indicates the median deviation and the black box the quartile range. The hinges on the side of the box extend from the side of the box to the data point that is closest to, but does not exceed, 1.5 times the interquartile range. The curves show the density of the distribution.

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