Computational identification of RNA motifs in genome sequences

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.