The rapid progression of genomics and proteomics has been driven by the advent of
advanced sequencing technologies, large, diverse, and readily available omics datasets …

The decrease in sequencing expenses has facilitated the creation of reference genomes
and proteomes for an expanding array of organisms. Nevertheless, no established …

An absent factor of a string w is a string u which does not occur as a contiguous substring
(aka factor) inside w. We extend this well-studied notion and define absent subsequences: a …

Minimal absent words (MAWs) are minimal-length oligomers absent from a genome or
proteome. Although some artificially synthesized MAWs have deleterious effects, there is still …

One of the main challenges in the diagnosis of infectious diseases is the need for rapid and
accurate detection of the causative pathogen in any setting. Rapid diagnosis is key to …

Motivation Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused
more than 14 million cases and more than half million deaths. Given the absence of …

Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is
often realised by sequence alignment techniques, which are computationally expensive …

String matching is one of the oldest algorithmic techniques, yet still one of the most
pervasive in computer science. The past 20 years have seen technological leaps in …

An absent word of a word y is a word that does not occur in y. It is then called minimal if all its
proper factors occur in y. In fact, minimal absent words (MAWs) provide useful information …

The directed acyclic word graph (DAWG) of a string y of length n is the smallest (partial) DFA
which recognizes all suffixes of y with only O (n) nodes and edges. In this paper, we show …