Related papers: Characterising the D2 statistic: word matches in b…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
We consider a component of the word statistics known as clump; starting from a finite set of words, clumps are maximal overlapping sets of these occurrences. This parameter has first been studied by Schbath with the aim of counting the…
Matched case-control studies are commonly employed in epidemiological research for their convenience and efficiency. Analysis of secondary outcomes can yield valuable insights into biological pathways and help identify genetic variants of…
Understanding how words change their meanings over time is key to models of language and cultural evolution, but historical data on meaning is scarce, making theories hard to develop and test. Word embeddings show promise as a diachronic…
Motivation: Alignment-free (AF) distance/similarity functions are a key tool for sequence analysis. Experimental studies on real datasets abound and, to some extent, there are also studies regarding their control of false positive rate…
Adaptations of features commonly applied in the field of visual computing, co-occurrence matrix (COM) and run-length matrix (RLM), are proposed for the similarity computation of strings in general (words, phrases, codes and texts). The…
Statistical matching is an effective method for estimating causal effects in which treated units are paired with control units with ``similar'' values of confounding covariates prior to performing estimation. In this way, matching helps…
Sequence comparison is a widely used computational technique in modern molecular biology. In spite of the frequent use of sequence comparisons the important problem of assigning statistical significance to a given degree of similarity is…
The nature of the alignment with gaps corresponding to a longest common subsequence (LCS) of two independent iid random sequences drawn from a finite alphabet is investigated. It is shown that such an optimal alignment typically matches…
Recent observations in the theory of verse and empirical metrics have suggested that constructing a verse line involves a pattern-matching search through a source text, and that the number of found elements (complete words totaling a…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
Sequence classification algorithms, such as SVM, require a definition of distance (similarity) measure between two sequences. A commonly used notion of similarity is the number of matches between $k$-mers ($k$-length subsequences) in the…
In this paper we consider several variants of the pattern matching problem. In particular, we investigate the following problems: 1) Pattern matching with k mismatches; 2) Approximate counting of mismatches; and 3) Pattern matching with…
What advantage do \emph{sequential} procedures provide over batch algorithms for testing properties of unknown distributions? Focusing on the problem of testing whether two distributions $\mathcal{D}_1$ and $\mathcal{D}_2$ on $\{1,\dots,…
Two words $w_1$ and $w_2$ are said to be $k$-binomial equivalent if every non-empty word $x$ of length at most $k$ over the alphabet of $w_1$ and $w_2$ appears as a scattered factor of $w_1$ exactly as many times as it appears as a…
We introduce a novel definition of approximate palindromes in strings, and provide an algorithm to find all maximal approximate palindromes in a string with up to $k$ errors. Our definition is based on the usual edit operations of…
Given a pattern string $P$ of length $n$ and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet of size $\Delta$, the {\em exact string matching} problem consists of finding all occurrences of…
A methodology is proposed to automatically detect significant symbol associations in genomic databases. A new statistical test is proposed to assess the significance of a group of symbols when found in several genesets of a given database.…
Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that…
Considering the optimal alignment of two i.i.d. random sequences of length $n$, we show that when the scoring function is chosen randomly, almost surely the empirical distribution of aligned letter pairs in all optimal alignments converges…