Related papers: Zimin patterns in genomes
Babson and Steingr\'{\i}msson introduced generalized permutation patterns that allow the requirement that two adjacent letters in a pattern must be adjacent in the permutation. We consider n-permutations that avoid the generalized pattern…
In this paper we study the enumeration and the construction, according to the number of ones, of particular binary words avoiding a fixed pattern. The growth of such words can be described by particular jumping and marked succession rules.…
Complexity metrics and machine learning (ML) models have been utilized to analyze the lengths of segmental genomic entities like: exons, introns, intergenic and repeat/unique DNA sequences, in each of the 22 human chromosomes. The purpose…
Coding information is the main source of heterogeneity (non-randomness) in the sequences of bacterial genomes. This information can be naturally modeled by analysing cluster structures in the "in-phase" triplet distributions of relatively…
The distribution of bases spacing in human genome was investigated. An analysis of the frequency of occurrence in the human genome of different sequence lengths flanked by one type of nucleotide was carried out showing that the distribution…
We enumerate permutations that avoid all but one of the $k$ patterns of length $k$ starting with a monotone increasing subsequence of length $k-1$. We compare the size of such permutation classes to the size of the class of permutations…
Pattern avoidance for permutations has been extensively studied, and has been generalized to vincular patterns, where certain elements can be required to be adjacent. In addition, cyclic permutations, i.e., permutations written in a circle…
We consider the enumeration of ordered set partitions avoiding a permutation pattern, as introduced by Godbole, Goyt, Herdan and Pudwell. Let $\op_{n,k}(p)$ be the number of ordered set partitions of $\{1,2,\ldots,n\}$ into $k$ blocks that…
This study focuses on efficient schemes for enumerative coding of $\sigma$--ary sequences by mainly borrowing ideas from \"Oktem & Astola's \cite{Oktem99} hierarchical enumerative coding and Schalkwijk's \cite{Schalkwijk72} asymptotically…
We study the effects of the sequence on the propagation of nonlinear excitations in simple models of DNA in which we incorporate actual DNA sequences obtained from human genome data. We show that kink propagation requires forces over a…
Genome-wide analysis of distributions of densities of long-range interactions of human chromosomes with each other, nucleoli, nuclear lamina, and binding sites of chromatin state regulatory proteins, CTCF and STAT1, identifies non-random…
In eukaryotic genes the protein coding sequence is split into several fragments, the exons, separated by non-coding DNA stretches, the introns. Prokaryotes do not have introns in their genome. We report the calculations of stability domains…
In [GM] Guibert and Mansour studied involutions on n letters avoiding (or containing exactly once) 132 and avoiding (or containing exactly once) an arbitrary pattern on k letters. They also established a bijection between 132-avoiding…
We prove that the number of permutations avoiding an arbitrary consecutive pattern of length m is asymptotically largest when the avoided pattern is 12...m, and smallest when the avoided pattern is 12...(m-2)m(m-1). This settles a…
We study the simple genetic algorithm with a ranking selection mechanism (linear ranking or tournament). We denote by $\ell$ the length of the chromosomes, by $m$ the population size, by $p_C$ the crossover probability and by $p_M$ the…
We show how to enumerate words in $1^{m_1} \dots n^{m_n}$ that avoid the increasing consecutive pattern $12 \dots r$ for any $r \geq 2$. Our approach yields an $O(n^{s+1})$ algorithm to enumerate words in $1^s \dots n^s$, avoiding the…
The nature of the quantitative distribution of the 64 DNA codons in the human genome has been an issue of debate for over a decade. Some groups have proposed that the quantitative distribution of the DNA codons ordered as a rank-frequency…
During evolution of microorganisms genomes underwork have different changes in their lengths, gene orders, and gene contents. Investigating these structural rearrangements helps to understand how genomes have been modified over time. Some…
Determining the full complement of protein-coding genes is a key goal of genome annotation. The most powerful approach for confirming protein coding potential is the detection of cellular protein expression through peptide mass spectrometry…
We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…