A novel approach to represent and compare RNA secondary structures

Structural information is crucial in ribonucleic acid (RNA) analysis and functional annotation; neverthe-less, how to include such structural data is still a de-bated problem. Dot-bracket notation is the most com-mon and simple representation for RNA secondary structures but its simplicity leads also to ambiguity requiring further processing steps to dissolve. Here we present BEAR (Brand nEw Alphabet for RNA), a new context-aware structural encoding represented by a string of characters. Each character in BEAR encodes for a specific secondary structure element (loop, stem, bulge and internal loop) with specific length. Furthermore, exploiting this informative and yet simple encoding in multiple alignments of related RNAs, we captured how much structural variation is tolerated in RNA families and convert it into tran-sition rates among secondary structure elements. This allowed us to compute a substitution matrix for secondary structure elements called MBR (Matrix of BEAR-encoded RNA secondary structures), of which we tested the ability in aligning RNA secondary struc-tures. We propose BEAR and the MBR as powerful resources for the RNA secondary structure analy-sis, comparison and classification, motif finding and phylogeny