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. Enumeration of protein contact maps has considerable difficulties due to the significant higher vertex degree than that of RNA secondary structures. The state of art maximum vertex degree in previous works is two. This paper proposes a solution for counting stacks in protein contact maps with arbitrary vertex degree upper bound. By establishing bijection between such general stacks and $m$-regular $\Lambda$-avoiding $DLU$ paths, and counting the paths using theories of pattern avoiding lattice paths, we obtain a unified system of equations for generating functions of general stacks. We also show that previous enumeration results for RNA secondary structures and protein contact maps can be derived from the unified equation system as special cases.