Abstract
Many small RNAs have known 2-D structural elements. The aim of the project is to search and identify new potential small RNAs and regulatory elements in genomic databases using known 2-D conformations. The first experimental implementation was to attempt to identify the yeast mitochondrial 5S rRNA in the yeast, Saccharomyces cerevisae, nuclear genome. A descriptor was designed to identify sequences that maintain most of the conserved elements in all known 5S rRNAs. This search identified only one compatible sequence in the yeast genome. This sequence fell within a non-coding region of chromosome V. Experimental verification of this RNA is being carried out. A second experiment is to identify RNase MRP/P homologs. A descriptor was designed to search for the highly conserved cage structure. Extensive use of distributed processors was made to perform this search, dividing the sequence database into smaller chunks of individual chromosomes.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Macke, T., Ecker, D., Gutell, D., Gautheret, D.A., Case, D.A., Sampath, D.A.: RNAMotif, an RNA secondary structure definition and search algorithm. Nucl. Acids Res. 29, 4724–4735 (2001)
Macke, T., Case, D.: RNAMotif User’s Manual, Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA (2001)
Dolinski, K., Balakrishnan, R., Christie, K.R., Costanzo, M.C., Dwight, S.S., Engel, S.R., Fisk, D.G., Hirschman, J.E., Hong, E.L., Issel-Tarver, L., Sethuraman, A., Theesfeld, C.L., Binkley, G., Lane, C., Schroeder, M., Dong, S., Weng, S., Andrada, R., Botstein, D., Cherry, J.M.: Saccharomyces Genome Database (2003), http://www.yeastgenome.org/
Bullerwell, C.E., Schnare, M.N., Gray, M.W.: Discovery and characterization of Acanthamoeba castellanii mitochhondrial 5S rRNA. RNA 9, 287–292 (2003)
Szymanski, M., Barciszweska, M.Z., Erdmann, V.A., Barciszweska, J.: 5S ribosomal RNA Database. Nucl. Acids Res. 30, 176–178 (2002)
Schmitt, M.E., Clayton, D.A.: Nuclear RNase MRP is required for correct processing of pre-5.8S rRNA in Saccharomyces cerevisiae. Mol. Cell. Biol. 13, 7935–7941 (1993)
Stohl, L.L., Clayton, D.A.: Saccharomyces cerevisiae contains an RNase MRP that cleaves at a conserved mitochondrial RNA sequence implicated in replication priming. Mol. Cell. Biol. 12, 2561–2569 (1992)
Forster, A.C., Altman, S.: Similar cage-shaped structure for the RNA components of all ribonuclease P and ribonuclease MRP enzymes. Cell 62, 407–409 (1990)
Schmitt, M.E., Bennett, J.L., Dairaghi, D.J., Clayton, D.A.: Secondary structure of RNase MRP RNA as predicted by phylogenetic comparison. FASEB J. 7, 208–213 (1993)
Schmitt, M.E.: Molecular modeling of the three-dimensional architecture of the RNA component of yeast RNase MRP. J. Mol. Biol. 292, 827–836 (1999)
Reilly, T.H., Schmitt, M.E.: The yeast, Saccharomyces cerevisiae, RNase P/MRP ribonucleoprotein endoribonuclease family. Mol. Biol. Reports 23, 87–93 (1996)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2004 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Narale, G., Beaumont, J., Rice, P.A., Schmitt, M.E. (2004). Computational Identification of RNA Motifs in Genome Sequences. In: Orchard, B., Yang, C., Ali, M. (eds) Innovations in Applied Artificial Intelligence. IEA/AIE 2004. Lecture Notes in Computer Science(), vol 3029. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-24677-0_15
Download citation
DOI: https://doi.org/10.1007/978-3-540-24677-0_15
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-22007-7
Online ISBN: 978-3-540-24677-0
eBook Packages: Springer Book Archive