Zigzag stacks and m-regular linear stacks

• Published in: Journal of computational biology Vol. 21; no. 12; p. 915
• Main Authors: Chen, William Y C, Guo, Qiang-Hui, Sun, Lisa H, Wang, Jian
• Format: Journal Article
• Language: English
• Published: United States 01.12.2014
• Subjects: Algorithms; Models, Molecular; RNA - chemistry; RNA Folding; Software; Thermodynamics; zigzag stack; contact map; m-regular linear stack; protein
• ISSN: 1557-8666
• DOI: 10.1089/cmb.2014.0133

The contact map of a protein fold is a graph that represents the patterns of contacts in the fold. It is known that the contact map can be decomposed into stacks and queues. RNA secondary structures are special stacks in which the degree of each vertex is at most one and each arc has length of at least two. Waterman and Smith derived a formula for the number of RNA secondary structures of length n with exactly k arcs. Höner zu Siederdissen et al. developed a folding algorithm for extended RNA secondary structures in which each vertex has maximum degree two. An equation for the generating function of extended RNA secondary structures was obtained by Müller and Nebel by using a context-free grammar approach, which leads to an asymptotic formula. In this article, we consider m-regular linear stacks, where each arc has length at least m and the degree of each vertex is bounded by two. Extended RNA secondary structures are exactly 2-regular linear stacks. For any m ≥ 2, we obtain an equation for the generating function of the m-regular linear stacks. For given m, we deduce a recurrence relation and an asymptotic formula for the number of m-regular linear stacks on n vertices. To establish the equation, we use the reduction operation of Chen, Deng, and Du to transform an m-regular linear stack to an m-reduced zigzag (or alternating) stack. Then we find an equation for m-reduced zigzag stacks leading to an equation for m-regular linear stacks.