Invited Talks
Maxime CrochemoreTitle: Fast detection of specific fragments against a set of sequences
We design alignment-free techniques for comparing a sequence or word, called a target, against a set of words, called a reference. A target-specific factor of a target $T$ against a reference $R$ is a factor $w$ of a word in $T$ which is not a factor of a word of $R$ and such that any proper factor of w is a factor of a word of $R$. We first address the computation of the set of target-specific factors of a target $T$ against a reference $R$, where $T$ and $R$ are finite sets of sequences. The result is the construction of an automaton accepting the set of all considered target-specific factors. The construction algorithm runs in linear time according to the size of $T \cup R$. The second result consists of the design of an algorithm to compute all the occurrences in a single sequence $T$ of its target-specific factors against a reference $R$. The algorithm runs in real-time on the target sequence, independently of the number of occurrences of target-specific factors.
Jakub Radoszewski
Title: Quasiperiodicity in Strings
Quasiperiodicity is a relaxed version of periodicity in strings. A \emph{cover} (also called quasiperiod) of a string $S$ is a substring of $S$ whose occurrences cover the whole string $S$. A \emph{seed} of $S$ is a cover of a superstring of $S$. In this talk I will review fundamental algorithms for computing covers and seeds from the 1990s and discuss selected recent and new results on non-standard notions of quasiperiodicity like internal covers and $\lambda$-covers. In particular, I will show how the ideas behind the classic algorithms can be applied to efficiently compute substring covers in the internal setting.
