Search for Conserved Secondary Structures of RNA

Byline: K. Yu. Gorbunov (1), A. A. Mironov (2), V. A. Lyubetsky (1) Keywords: RNA secondary structure; algorithm of dynamic programming; tRNA structure; RFN structure; regulation of transcription; regulation of translation Abstract: We suggest a new algorithm to search a given set of the RNA sequences for conserved secondary structures. The algorithm is based on alignment of the sequences for potential helical strands. This procedure can be used to search for new structured RNAs and new regulatory elements. It is efficient for the genome-scale analysis. The results of various tests run with this algorithm are shown. Author Affiliation: (1) Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 101447, Russia (2) State Research Center GosNIIGenetika, Moscow, 113545, Russia Article History: Registration Date: 12/10/2004