Related papers: Motzkin path on RNA abstract shapes
A quantitative characterization of the relationship between molecular sequence and structure is essential to improve our understanding of how function emerges. This particular genotype-phenotype map has been often studied in the context of…
Combinatorial analysis of a certain abstract of RNA structures has been studied to investigate their statistics. Our approach regards the backbone of secondary structures as an alternate sequence of paired and unpaired sets of nucleotides,…
RNA molecules are known to form complex secondary structures including pseudoknots. A systematic framework for the enumeration, classification and prediction of secondary structures is critical to determine the biological significance of…
In this paper we derive the generating function of RNA structures with pseudoknots. We enumerate all $k$-noncrossing RNA pseudoknot structures categorized by their maximal sets of mutually intersecting arcs. In addition we enumerate…
We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for…
We give recurrence relations for the enumeration of symmetric elements within four classes of arc diagrams corresponding to certain involutions and set partitions whose blocks contain no consecutive integers. These arc diagrams are…
In this paper we study abstract shapes of $k$-noncrossing, $\sigma$-canonical RNA pseudoknot structures. We consider ${\sf lv}_k^{\sf 1}$- and ${\sf lv}_k^{\sf 5}$-shapes, which represent a generalization of the abstract $\pi'$- and…
We propose a new topological characterization of RNA secondary structures with pseudoknots based on two topological invariants. Starting from the classic arc-representation of RNA secondary structures, we consider a model that couples both…
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…
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…
This paper is motivated by two problems recently proposed by Coker on combinatorial identities related to the Narayana polynomials and the Catalan numbers. We find that a bijection of Chen, Deutsch and Elizalde can be used to provide…
RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two…
In this paper we study properties of topological RNA structures, i.e.~RNA contact structures with cross-serial interactions that are filtered by their topological genus. RNA secondary structures within this framework are topological…
We present a novel topological classification of RNA secondary structures with pseudoknots. It is based on the topological genus of the circular diagram associated to the RNA base-pair structure. The genus is a positive integer number,…
We give a combinatorial interpretation of a matrix identity on Catalan numbers and the sequence $(1, 4, 4^2, 4^3, ...)$ which has been derived by Shapiro, Woan and Getu by using Riordan arrays. By giving a bijection between weighted partial…
Large RNA molecules often carry multiple functional domains whose spatial arrangement is an important determinant of their function. Pre-mRNA splicing, furthermore, relies on the spatial proximity of the splice junctions that can be…
There exists many complicated $k$-noncrossing pseudoknot RNA structures in nature based on some special conditions. The special characteristic of RNA structures gives us great challenges in researching the enumeration, prediction and the…
Two subclasses of Motzkin paths, S-Motzkin and T-Motzkin paths, are introduced. We provide bijections between S-Motzkin paths and ternary trees, S-Motzkin paths and non-crossing trees, and T-Motzkin paths and ordered pairs of ternary trees.…
We view the folding of RNA-sequences as a map that assigns a pattern of base pairings to each sequence, known as secondary structure. These preimages can be constructed as random graphs (i.e. the neutral networks associated to the structure…
We use the inversion of coefficient arrays to define dual polynomials to the Fibonacci and Catalan-Fibonacci polynomials, and we explore the properties of these new polynomials sequences. Many of the arrays involved are Riordan arrays.…