  The primary structure of a ribonucleic acid (RNA) molecule can be represented
as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The
secondary or tertiary structure of an RNA is a set of base pairs which form
bonds between A-U and G-C. For secondary structures, these bonds have been
traditionally assumed to be one-to-one and non-crossing. This paper considers
pattern matching as well as local alignment between two RNA structures. For
pattern matching, we present two algorithms, one for obtaining an exact match,
the other for approximate match. We then present an algorithm for RNA local
structural alignment.
