Bijective enumeration of general stacks

Abstract

Combinatorial enumeration of various RNA secondary structures and protein contact maps is of great interest for both combinatorists and computational biologists. Counting protein contact maps is much more difficult than that of RNA secondary structures due to the significant higher vertex degree. The state of art upper bound for vertex degree in previous works is two. This paper proposes a solution for counting general stacks with arbitrary vertex degree upper bound. By establishing a bijection between such general stacks and m-regular Λ-avoiding DLU-paths, and counting these pattern avoiding lattice paths, we obtain a unified system of equations for the generating functions of the number of general stacks. We further show that previous enumeration results for RNA secondary structures and linear stacks of protein contact maps can be derived from the equations for general stacks as special cases.