NMR solution structure of a parallel LNA quadruplex

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NMR solution structure of a parallel LNA quadruplex

Oxford University Press
DOI: 10.1093/nar/gkh629
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gkm160 3100..3108 3100–3108 Nucleic Acids Research, 2007, Vol. 35, No. 9 Published online 22 April 2007 doi:10.1093/nar/gkm160 RNAmmer: consistent and rapid annotation of ribosomal RNA genes Karin Lagesen1,2,*, Peter Hallin3, Einar Andreas Rødland1,2,4,5, Hans-Henrik Stærfeldt3, Torbjørn Rognes1,2,4 and David W. Ussery1,2,3 1Centre for Molecular Biology and Neuroscience and Institute of Medical Microbiology, University of Oslo, NO-0027 Oslo, Norway, 2Centre for Molecular Biology and Neuroscience and Institute of Medical Microbiology, Rikshospitalet-Radiumhospitalet Medical Centre, NO-0027 Oslo, Norway, 3Center for Biological Sequence Analysis, Biocentrum-DTU, Technical University of Denmark, DK-2800 Lyngby, Denmark, 4Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316 Oslo, Norway and 5Norwegian Computing Center, PO Box 114 Blindern, NO-0314 Oslo, Norway Received December 1, 2006; Revised and Accepted March 2, 2007 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 incon- sistently 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. INTRODUCTION Ribosomes are the molecu

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