Related papers: Motzkin path on RNA abstract shapes
In the first part of this paper I give an elementary overview about some number sequences which count various sorts of lattice paths in strips along the x-axis and compute their generating functions in terms of Fibonacci and Lucas…
We introduce an equivalence relation on the set of Dyck paths and some operations on them. We determine a formula for the cardinality of those equivalence classes and use this information to obtain a combinatorial formula for the number of…
We establish an explicit combinatorial/homological characterization of supports for linear degenerations of flag varieties. For such purpose, we introduce the concept of an excessive multisegment. It provides a new class of combinatorial…
RNA folding prediction remains challenging, but can be also studied using a topological mathematical approach. In the present paper, the mathematical method to compute the topological classification of RNA structures and based on matrix…
In this paper we derive polynomial time algorithms that generate random $k$-noncrossing matchings and $k$-noncrossing RNA structures with uniform probability. Our approach employs the bijection between $k$-noncrossing matchings and…
We find a generating function for interval-closed sets of the product of two chains poset by constructing a bijection to certain bicolored Motzkin paths. We also find a functional equation for the generating function of interval-closed sets…
In many applications of shape analysis, lengths between some landmarks are constrained. For instance, biomolecules often have some bond lengths and some bond angles constrained, and variation occurs only along unconstrained bonds and…
We provide new interpretations for a subset of Raney numbers, involving threshold sequences and Motzkin-like paths with long up and down steps. Given three integers n, k, l such that n >= 1, k >= 2 and 0 <= l <= k-2, a (k,l)-threshold…
Counting the number of permutations of a given total displacement is equivalent to counting weighted Motzkin paths of a given area (Guay-Paquet and Petersen, 2014). The former combinatorial problem is still open. In this work, we show that…
We propose a lattice model for RNA based on a self-interacting two-tolerant trail. Self-avoidance and elements of tertiary structure are taken into account. We investigate a simple version of the model in which the native state of RNA…
We consider various classes of Motzkin trees as well as lambda-terms for which we derive asymptotic enumeration results. These classes are defined through various restrictions concerning the unary nodes or abstractions, respectively: We…
RNA forms elaborate secondary structures through intramolecular base pairing. These structures perform critical biological functions within each cell. Due to the availability of a polynomial algorithm to calculate the partition function…
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…
Two subfamilies of Motzkin paths, with the same numbers of up, down, horizontal steps were known to be equinumerous with ternary trees and related objects. We construct a bijection between these two families that does not use any auxiliary…
We introduce a novel fully convolutional neural network (FCN) architecture for predicting the secondary structure of ribonucleic acid (RNA) molecules. Interpreting RNA structures as weighted graphs, we employ deep learning to estimate the…
We extend an hypergraph representation, introduced by Finkelstein and Roytberg, to unify dynamic programming algorithms in the context of RNA folding with pseudoknots. Classic applications of RNA dynamic programming energy minimization,…
We establish three identities involving Dyck paths and alternating Motzkin paths, whose proofs are based on variants of the same bijection. We interpret these identities in terms of closed random walks on the halfline. We explain how these…
We investigate paths in the hexagonal circle packing and enumerate them with respect to width, height, number of steps, area, and kissing number. Functional equations and the kernel method yield closed bivariate generating functions…
It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from…
A k-noncrossing RNA pseudoknot structure is a graph over $\{1,...,n\}$ without 1-arcs, i.e. arcs of the form (i,i+1) and in which there exists no k-set of mutually intersecting arcs. In particular, RNA secondary structures are 2-noncrossing…