RNA-RNA Interaction Prediction and Antisense RNA Target Search

Abstract. Recent studies demonstrating the existence of special non-coding "antisense" RNAs used in post-transcriptional gene regulation have received considerable attention. These RNAs are synthesized naturally to control gene expression in C.elegans, Drosophila and other organisms; they are known to regulate plasmid copy numbers in E.coli as well. Small RNAs have also been artificially constructed to knock-out genes of interest in humans and other organisms for the purpose of finding out more about their functions. Although there are a number of algorithms for predicting the secondary structure of a single RNA molecule, no such algorithm exists for reliably predicting the joint secondary structure of two interacting RNA molecules, or measuring the stability of such a joint structure. In this paper, we describe the RNA-RNA interaction prediction (RIP) problem between an antisense RNA and its target mRNA and develop efficient algorithms to solve it. Our algorithms minimize th...

• Type: Conference
• Year: 2005
• Where: RECOMB
• Authors: Can Alkan, Emre Karakoç, Joseph H. Nadeau, Süleyman Cenk Sahinalp, Kaizhong Zhang
• Keywords: Associated Genome Sequence, Computational Biology, RECOMB 2005, RNA Molecules, RNA-RNA Interaction Prediction