General enumeration of RNA secondary structures based on new arc representation

Abstract

We have presented a new arc representation, which differentiates the Watson-Crick base pairs between AU and GC. Based on the new representation, this paper also computes the number of various types of constrained secondary structures taking the minimum stack length 1 and minimum size m for each bonding loop as two parameters by virtue of the technique of generating function. Furthermore, asymptotes are derived from these recurrences relations, which are the generalizations of previous results.

Keywords: RNA secondary structure, recurrence relation, generating function, asymptotic enumeration

African Journal of Biotechnology Vol. 12(14), pp. 1576-1584