http://precedings.nature.com/tags/RNA%20secondary%20structure Recently posted documents tagged with 'RNA secondary structure' Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://precedings.nature.com/documents/3561/version/1 Biomedical Ontologies are intended to integrate diverse biomedical data to enable intelligent data-mining and facilitate translation of basic research into useful clinical knowledge. We present the first version of RNAO, an ontology for integrating RNA 3D structural, biochemical and sequence data. While each 3D data file depicts the structure of a specific molecule, such data have broader significance as representatives of classes of homologous molecules, which, while differing in sequence, generally share core structural features of functional importance. Thus, 3D structure data gain value by being linked to homologous sequences in genomic data and databases of sequence alignments. Likewise genomic data can increase in value by annotation of shared structural features, especially when these can be linked to specific functions. The RNAO is being developed in line with the developing standards of the Open Biomedical Ontologies (OBO) Consortium. http://precedings.nature.com/documents/3561/version/1 Thu, 06 Aug 2009 11:30:04 UTC The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data hdl:10101/npre.2009.3561.1 2009-08-06 Colin Batchelor Nature Precedings 2009-08-06T11:30:04Z Manuscript Chemistry Genetics & Genomics Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/1248/version/1 The search for mechanisms of translational regulation has yielded many experimentally identified internal ribosome entry sites (IRES). Because of the lack of sequence similarity among the experimentally IRESs, it is widely assumed that IRESs posses stable secondary structure allowing them to interact with the components of the translation machinery. Contrary to this view, here we show that IRES activity in nine yeast IRESs, mapped to 60 nt immediately upstream of the initiation AUG, is strongly associated with the lack of secondary structure of IRESs. Furthermore, the reverse complements of these IRESs, with their secondary structure more stable than those of the IRESs, exhibit little IRES activity. The generality of this association is exemplified by the observation that, in the natural vpu-env bicistronic mRNA in HIV-1, the mRNA segment (60 nt) immediately upstream of the initiation AUG of env has the weakest secondary structure among all dominant HIV-1 mRNA species. These results suggest a unified model of alternative translation initiation. http://precedings.nature.com/documents/1248/version/1 Tue, 23 Oct 2007 15:17:56 UTC Internal ribosomal entry site lacks secondary structure hdl:10101/npre.2007.1248.1 2007-10-23 Xuhua Xia Nature Precedings 2007-10-23T15:17:56Z Manuscript Microbiology Molecular Cell Biology Bioinformatics http://creativecommons.org/licenses/by/2.5/