Related papers: RNA secondary structure design
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…
Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…
RNA design is the search for a sequence or set of sequences that will fold into predefined structures, also known as the inverse problem of RNA folding. While numerous RNA design methods have been invented to find sequences capable of…
In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete…
An RNA secondary structure is designable if there is an RNA sequence which can attain its maximum number of base pairs only by adopting that structure. The combinatorial RNA design problem, introduced by Hale\v{s} et al. in 2016, is to…
RNA design aims to find a sequence that folds with highest probability into a designated target structure. However, certain structures are undesignable, meaning no sequence can fold into the target structure under the default (Turner) RNA…
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…
RNA design aims to identify RNA sequences that fold into a target secondary structure. This task is challenging in terms of computational efficiency. Most existing methods focus on either minimum free energy (MFE)-based or ensemble-based…
In this work, we investigate a challenging problem, which has been considered to be an important criterion in designing codewords for DNA computing purposes, namely secondary structure avoidance in single-stranded DNA molecules. In short,…
In this paper, we propose an end-to-end deep learning model, called E2Efold, for RNA secondary structure prediction which can effectively take into account the inherent constraints in the problem. The key idea of E2Efold is to directly…
In this paper, we consider the problem of designing DNA sequences (codewords) for DNA storage systems and DNA computing that are unlikely to fold back onto themselves to form undesirable secondary structures. The paper addresses both the…
We construct a minimalist model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four or six-letter alphabets. With only two…
We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the…
The paper investigates the computational problem of predicting RNA secondary structures. The general belief is that allowing pseudoknots makes the problem hard. Existing polynomial-time algorithms are heuristic algorithms with no…
It is the first step for understanding how RNA structure folds from base sequences that to know how its secondary structure is formed. Traditional energy-based algorithms are short of precision, particularly for non-nested sequences, while…
In this paper we study irreducibility in RNA structures. By RNA structure we mean RNA secondary as well as RNA pseudoknot structures. In our analysis we shall contrast random and minimum free energy (mfe) configurations. We compute various…
Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These…
Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These…
RNA secondary structure prediction and classification are two important problems in the field of RNA biology. Here, we propose a new permutation based approach to create logical non-disjoint clusters of different secondary structures of a…