Related papers: Pattern Matching and Local Alignment for RNA Struc…
We consider the Combinatorial RNA Design problem, a minimal instance of RNA design where one must produce an RNA sequence that adopts a given secondary structure as its minimal free-energy structure. We consider two free-energy models where…
A representation of the genetic code as a six-dimensional Boolean hypercube is proposed. It is assumed here that this structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition.…
Fabrication of DNA nanostructures primarily follows two fundamental rules. First, DNA oligonucleotides mutually combine by Watson-Crick base pairing rules between complementary base sequences. Second, the geometrical compatibility of the…
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 the combinatorial set of RNA secondary structures of length $n$ with $m$ base-pairs. For a compact representation, we encode an RNA secondary structure by the corresponding Motzkin word. For this combinatorial set,…
Graph are a ubiquitous data representation, as they represent a flexible and compact representation. For instance, the 3D structure of RNA can be efficiently represented as $\textit{2.5D graphs}$, graphs whose nodes are nucleotides and…
RNA secondary structures prediction is one of the main issues in bioinformatics. It seeks to elucidate structural conserved regions within a set of RNA sequences. Unfortunately, finding an accurate conserved structure is a very hard task to…
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. We mine the evolutionary sequence record to derive precise information about function and…
A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex…
The three-dimensional conformations of non-coding RNAs underpin their biochemical functions but have largely eluded experimental characterization. Here, we report that integrating a classic mutation/rescue strategy with high-throughput…
RNAs self-interact through hydrogen-bond base-pairing between nucleotides and fold into specific, stable structures that substantially govern their biochemical behaviour. Experimental characterization of these structures remains difficult,…
It is a classical result of Stein and Waterman that the asymptotic number of RNA secondary structures is $1.104366 \cdot n^{-3/2} \cdot 2.618034^n$. Motivated by the kinetics of RNA secondary structure formation, we are interested in…
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…
Despite the biological importance of non-coding RNA, their structural characterization remains challenging. Making use of the rapidly growing sequence databases, we analyze nucleotide coevolution across homologous sequences via…
X-ray data indicate that complexes of ribosomes with cognate and near cognate tRNAs are very similar structurally, and this was the ground for a suggestion that the ribosome discriminates correct codon-anticodon pair because of its higher…
Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…
The alignment between RNA sequences and structures in foundation models (FMs) has yet to be thoroughly investigated. Existing FMs have struggled to establish sequence-structure alignment, hindering the free flow of genomic information…
Large Artificial Neural Network (ANN) models have demonstrated success in various domains, including general text and image generation, drug discovery, and protein-RNA (ribonucleic acid) binding tasks. However, these models typically demand…
The frequencies of A, C, G and T in mitochondrial DNA vary among species due to unequal rates of mutation between the bases. The frequencies of bases at four-fold degenerate sites respond directly to mutation pressure. At 1st and 2nd…
Accurate prediction of RNA three-dimensional (3D) structure remains an unsolved challenge. Determining RNA 3D structures is crucial for understanding their functions and informing RNA-targeting drug development and synthetic biology design.…