Related papers: Theta palindromes in theta conjugates
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
We study $I(T)$, the number of inversions in a tree $T$ with its vertices labeled uniformly at random, which is a generalization of inversions in permutations. We first show that the cumulants of $I(T)$ have explicit formulas involving the…
In highly repetitive strings, like collections of genomes from the same species, distinct measures of repetition all grow sublinearly in the length of the text, and indexes targeted to such strings typically depend only on one of these…
Mining gene expression profiles has proven valuable for identifying signatures serving as surrogates of cancer phenotypes. However, the similarities of such signatures across different cancer types have not been strong enough to conclude…
In this paper we investigate the endomorphism algebras of standard cluster tilting objects in the stably 2-Calabi-Yau categories $\Sub{\Lambda_w}$ with elements $w$ in Coxeter groups in \cite{BIRSc}. They are examples of the 2-Auslander…
Palindromes are strings that read the same forward and backward. Problems of computing palindromic structures in strings have been studied for many years with a motivation of their application to biology. The longest palindrome problem is…
A dictionary is a set of finite words over some finite alphabet X. The omega-power of a dictionary V is the set of infinite words obtained by infinite concatenation of words in V. Lecomte studied in [Omega-powers and descriptive set theory,…
A gapped repeat (respectively, palindrome) occurring in a word $w$ is a factor $uvu$ (respectively, $u^Rvu$) of $w$. In such a repeat (palindrome) $u$ is called the arm of the repeat (respectively, palindrome), while $v$ is called the gap.…
We propose that the distribution of DNA words in genomic sequences can be primarily characterized by a double Pareto-lognormal distribution, which explains lognormal and power-law features found across all known genomes. Such a distribution…
Compact directed acyclic word graphs (CDAWGs) [Blumer et al. 1987] are a fundamental data structure on strings with applications in text pattern searching, data compression, and pattern discovery. Intuitively, the CDAWG of a string $T$ is…
We study word reconstruction problems. Improving a previous result by P. Fleischmann, M. Lejeune, F. Manea, D. Nowotka and M. Rigo, we prove that, for any unknown word $w$ of length $n$ over an alphabet of cardinality $k$, $w$ can be…
In this paper we consider the palindromes that can be formed by taking unordered sets of $n$ elements from an alphabet of $b$ letters. In particular, we seek to find the probability that given a random member of this space we are able to…
This paper reviews some results regarding symbolic dynamics, correspondence between languages of dynamical systems and combinatorics. Sturmian sequences provide a pattern for investigation of one-dimensional systems, in particular interval…
We study the palindromic complexity of infinite words $u_\beta$, the fixed points of the substitution over a binary alphabet, $\phi(0)=0^a1$, $\phi(1)=0^b1$, with $a-1\geq b\geq 1$, which are canonically associated with quadratic non-simple…
We say that a family $\mathcal{W}$ of strings over $\Sigma^+$ forms a Unique Maximal Factorization Family (UMFF) if and only if every $w \in \mathcal{W}$ has a unique maximal factorization. Further, an UMFF $\mathcal{W}$ is called a…
The theoretical study of deformability of special sequence of DNA double helix TATA-box is presentated. The paper elaborates on the mechanisms of abnormal deformation of DNA TATA-box double helix that cannot be explained using the standard…
The main theme of this paper is the enumeration of the occurrence of a pattern in words and permutations. We mainly focus on asymptotic properties of the sequence $f_r^v(k,n),$ the number of $n$-array $k$-ary words that contain a given…
We calculate the probability distribution of repetitions of ancestors in a genealogical tree for simple neutral models of a closed population with sexual reproduction and non-overlapping generations. Each ancestor at generation g in the…
The Burrows-Wheeler-Transform (BWT) is a reversible string transformation which plays a central role in text compression and is fundamental in many modern bioinformatics applications. The BWT is a permutation of the characters, which is in…
We study the iterated Galton-Watson process (IGW), possibly with thinning, introduced by Gawe{\l}and Kimmel to model the number of repeats of DNA triplets during some genetic disorders. If the process involves some thinning, then extinction…