Kristin Missal1, Dominic Rose, Peter F Stadler. 1. Bioinformatics Group, Department of Computer Science, University of Leipzig, Germany. kristin@bioinf.uni-leipzig.de
Abstract
MOTIVATION: The analysis of animal genomes showed that only a minute part of their DNA codes for proteins. Recent experimental results agree, however, that a large fraction of these genomes are transcribed and hence are probably functional at the RNA level. A computational survey of vertebrate genomes has predicted thousands of previously unknown ncRNAs with evolutionarily conserved secondary structures. Extending these comparative studies beyond vertebrates is difficult, however, since most ncRNAs evolve quickly at the sequence level while conserving their characteristic secondarystructures. RESULTS: We report on a computational screen of structured ncRNAs in the urochordate lineage based on a comparison of the genomic data from Ciona intestinalis, Ciona savignyi and Oikopleura dioica. We predict >1000 ncRNAs with an evolutionarily conserved RNA secondary structure. Of these, about a quarter are located in introns of known protein coding sequences. A few RNA motifs can be identified as known RNAs, including approximately 300 tRNAs, some 100 snRNA genes and a few microRNAs and snoRNAs. AVAILABILITY: www.bioinf.uni-leipzig.de/Publications/SUPPLEMENTS/05-008/
MOTIVATION: The analysis of animal genomes showed that only a minute part of their DNA codes for proteins. Recent experimental results agree, however, that a large fraction of these genomes are transcribed and hence are probably functional at the RNA level. A computational survey of vertebrate genomes has predicted thousands of previously unknown ncRNAs with evolutionarily conserved secondary structures. Extending these comparative studies beyond vertebrates is difficult, however, since most ncRNAs evolve quickly at the sequence level while conserving their characteristic secondarystructures. RESULTS: We report on a computational screen of structured ncRNAs in the urochordate lineage based on a comparison of the genomic data from Ciona intestinalis, Ciona savignyi and Oikopleura dioica. We predict >1000 ncRNAs with an evolutionarily conserved RNA secondary structure. Of these, about a quarter are located in introns of known protein coding sequences. A few RNA motifs can be identified as known RNAs, including approximately 300 tRNAs, some 100 snRNA genes and a few microRNAs and snoRNAs. AVAILABILITY: www.bioinf.uni-leipzig.de/Publications/SUPPLEMENTS/05-008/
Authors: Stephan H Bernhart; Hakim Tafer; Ulrike Mückstein; Christoph Flamm; Peter F Stadler; Ivo L Hofacker Journal: Algorithms Mol Biol Date: 2006-03-16 Impact factor: 1.405
Authors: Claudia S Copeland; Manja Marz; Dominic Rose; Jana Hertel; Paul J Brindley; Clara Bermudez Santana; Stephanie Kehr; Camille Stephan-Otto Attolini; Peter F Stadler Journal: BMC Genomics Date: 2009-10-08 Impact factor: 3.969
Authors: Jana Hertel; Danielle de Jong; Manja Marz; Dominic Rose; Hakim Tafer; Andrea Tanzer; Bernd Schierwater; Peter F Stadler Journal: Nucleic Acids Res Date: 2009-01-16 Impact factor: 16.971