Related papers: Zimin patterns in genomes
String Kernel (SK) techniques, especially those using gapped $k$-mers as features (gk), have obtained great success in classifying sequences like DNA, protein, and text. However, the state-of-the-art gk-SK runs extremely slow when we…
Minimizers sampling is one of the most widely-used mechanisms for sampling strings [Roberts et al., Bioinformatics 2004]. Let $S=S[1]\ldots S[n]$ be a string over a totally ordered alphabet $\Sigma$. Further let $w\geq 2$ and $k\geq 1$ be…
Sergey Kitaev has shown that the exponential generating function for permutations avoiding the generalized pattern $\sigma$-$k$, where $\sigma$ is a pattern without dashes and $k$ is one greater than the biggest element in $\sigma$, is…
Among all insect genomes, honeybee displays one of the most unusual patterns with interspersed long AT and GC-rich segments. Nearly 75% of the protein-coding genes are located in the AT-rich segments of the genome, but the biological…
Word $W$ is an instance of word $V$ provided there is a homomorphism $\phi$ mapping letters to nonempty words so that $\phi(V) = W$. For example, taking $\phi$ such that $\phi(c)=fr$, $\phi(o)=e$ and $\phi(l)=zer$, we see that "freezer" is…
A key aim in biology and psychology is to identify fundamental principles underpinning the behavior of animals, including humans. Analyses of human language and the behavior of a range of non-human animal species have provided evidence for…
The minimizer of a word of size $k$ (a $k$-mer) is defined as its smallest substring of size $m$ (with $m\leq k$), according to some ordering on $m$-mers. minimizers have been used in bioinformatics -- notably -- to partition sequencing…
Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…
Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…
A permutation $\pi$ contains a pattern $\sigma$ if and only if there is a subsequence in $\pi$ with its letters are in the same relative order as those in $\sigma$. Partially ordered patterns (POPs) provide a convenient way to denote…
A prefix normal word is a binary word with the property that no substring has more 1s than the prefix of the same length. This class of words is important in the context of binary jumbled pattern matching. In this paper we present an…
We prove new results concerning the relation between bifix codes, episturmian words and subgroups offree groups. We study bifix codes in factorial sets of words. We generalize most properties of ordinary maximal bifix codes to bifix codes…
A permutation $\pi$ is said to avoid a chain $(\sigma:\tau)$ of patterns if $\pi$ avoids $\sigma$ and $\pi^2$ avoids $\tau.$ In this paper, we define a notion of pattern avoidance for compositions of positive integers and use that idea to…
In the last decade a huge amount of articles has been published studying pattern avoidance on permutations. From the point of view of enumeration, typically one tries to count permutations avoiding certain patterns according to their…
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,…
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 sets of natural…
We present a new class of binary words: the prefix normal words. They are defined by the property that for any given length $k$, no factor of length $k$ has more $a$'s than the prefix of the same length. These words arise in the context of…
In 2011, Fici and Lipt\'ak introduced prefix normal words. A binary word is prefix normal if it has no factor (substring) that contains more occurrences of the letter 1 than the prefix of the same length. Among the open problems regarding…
Proteins are constructed from a limited alphabet of ~20 amino acids, yet the origins and selection of this specific alphabet are unresolved. One largely overlooked aspect is whether elemental composition constrains the range of viable…
Many commonly studied species now have more than one chromosome-scale genome assembly, revealing a large amount of genetic diversity previously missed by approaches that map short reads to a single reference. However, many species still…