A method for aligning RNA secondary structures and its application to RNA motif detection

Background: Alignment of RNA secondary structures is important in studying functional RNA motifs. In recent years, much progress has been made in RNA motif finding and structure alignment. However, existing tools either require a large number of prealigned structures or suffer from high time complexities. This makes it difficult for the tools to process RNAs whose prealigned structures are unavailable or process very large RNA structure databases. Results: We present here an efficient tool called RSmatch for aligning RNA secondary structures and for motif detection. Motivated by widely used algorithms for RNA folding, we decompose an RNA secondary structure into a set of atomic structure components that are further organized by a tree model to capture the structural particularities. RSmatch can find the optimal global or local alignment between two RNA secondary structures using two scoring matrices, one for singlestranded regions and the other for double-stranded regions. The time co...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Jianghui Liu, Jason Tsong-Li Wang, Jun Hu, Bin Tian
• Keywords: BMCBI 2005, Functional Rna Motifs, RNA Motifs, RNA Secondary Structures