Algorithms for searching RNA motifs in genomic sequences

With the progress of genome projects, a vast amount of nucleotide sequence data is now available, which makes it possible to study the species-specific gene expression systems involving transcription and translation for a wide range of organisms. Biological experiments indicate that functional RNAs have characteristic RNA structural motifs represented by specific combinations of base pairings and conserved nucleotides in the loop regions. The searching for those well-ordered RNA structures and their homologues in genomic sequences is very helpful for the understanding of RNA-based gene regulation. In this study, we consider the following problem: Given an RNA sequence with a known secondary structure, efficiently determine candidate segments in a given genomic sequence that can potentially form RNA secondary structures similar to the given RNA secondary structure. We search all potential stem-loops similar to ones of the given RNA secondary structure first, then based on located stem-loops, we propose an efficient bottom-up algorithm to detect potential homologous structural RNAs in the complete genome.