Related papers: Zimin patterns in genomes
The nucleotide composition of human genes with a special emphasis on transcription-related strand asymmetries is analyzed. Such asymmetries may be associated with different mutational rates in two principal factors. The first one is…
One of the ubiquitous representation of long DNA sequence is dividing it into shorter k-mer components. Unfortunately, the straightforward vector encoding of k-mer as a one-hot vector is vulnerable to the curse of dimensionality. Worse yet,…
Common intervals have been defined as a modelisation of gene clusters in genomes represented either as permutations or as sequences. Whereas optimal algorithms for finding common intervals in permutations exist even for an arbitrary number…
An infinte word w avoids a pattern p with the involution t if there is no substitution for the variables in p and no involution t such that the resulting word is a factor of w. We investigate the avoidance of patterns with respect to the…
We provide, on an extensive dataset and using several different distances, confirmation of the hypothesis that CGR patterns are preserved along a genomic DNA sequence, and are different for DNA sequences originating from genomes of…
Gene expression prediction, which predicts mRNA expression levels from DNA sequences, presents significant challenges. Previous works often focus on extending input sequence length to locate distal enhancers, which may influence target…
Every set of natural numbers determines a generating function convergent for $q \in (-1,1)$ whose behavior as $q \rightarrow 1^-$ determines a germ. These germs admit a natural partial ordering that can be used to compare sizes of sets of…
The well-known dictionary-based algorithms of the Lempel-Ziv (LZ) 77 family are the basis of several universal lossless compression techniques. These algorithms are asymmetric regarding encoding/decoding time and memory requirements, with…
Motivated by recent experiments probing shape, size and dynamics of bacterial chromosomes in growing cells, we consider a polymer model consisting of a circular backbone to which side-loops are attached, confined to a cylindrical cell. Such…
The avoidability, or unavoidability of patterns in words over finite alphabets has been studied extensively. A word (pattern) over a finite set is said to be unavoidable if, for all but finitely many words, there exists a morphism mapping…
The time required to transcribe genes with long primary transcripts may limit their ability to be expressed in cells with short mitotic cycles, a phenomenon termed intron delay. As such short cycles are a hallmark of the earliest stages of…
A novel scheme is introduced to capture the spatial correlations of consecutive amino acids in naturally occurring proteins. This knowledge-based strategy is able to carry out optimally automated subdivisions of protein fragments into…
The breakthrough performance of large language models (LLMs) comes with major computational footprints and high deployment costs. In this paper, we progress towards resolving this problem by proposing a novel structured compression approach…
In this paper, we present a novel design strategy of DNA codes with length $3n$ over the non-chain ring $R=\mathbb{Z}_4+u\mathbb{Z}_4+u^2\mathbb{Z}_4$ with $64$ elements and $u^3=1$, where $n$ denotes the length of a code over $R$. We first…
In Keck HIRES spectra of 9 QSOs we identify a sample of 908 CIV absorber components in 188 systems outside the Lyman forest in the redshift range 1.6 < z < 4.4, with related lines of SiIV, CII, SiII and NV. The properties of the CIV…
Genetic algorithms are a well-known method for tackling the problem of variable selection. As they are non-parametric and can use a large variety of fitness functions, they are well-suited as a variable selection wrapper that can be applied…
Motivated by the concept of partial words, we introduce an analogous concept of partial permutations. A partial permutation of length n with k holes is a sequence of symbols $\pi = \pi_1\pi_2 ... \pi_n$ in which each of the symbols from the…
We present a simple structure based model of how words are formed from morphemes. The model explains two major empirical facts: the typical distribution of word lengths and the appearance of Zipf like rank frequency curves. In contrast to…
The recently discovered Acanthamoeba polyphaga Mimivirus is the largest known DNA virus. Its particle size (>400 nm), genome length (1.2 million bp) and large gene repertoire (911 protein coding genes) blur the established boundaries…
Biological data mainly comprises of Deoxyribonucleic acid (DNA) and protein sequences. These are the biomolecules which are present in all cells of human beings. Due to the self-replicating property of DNA, it is a key constitute of genetic…