An EU funded network launched in 2021.
The hierarchical overlap graph (HOG for short) is an overlap encoding graph that efficiently represents overlaps from a given set $P$ of $n$ strings. A previously known algorithm constructs the HOG in $O(|| P || + n^2)$ time and $O(|| P || +n times …
Chaining fragments is a crucial step in genome alignment. Existing chaining algorithms compute a maximum weighted chain with no overlaps allowed between adjacent fragments. In practice, using local alignments as fragments, instead of MEMs, generates …
Motivation: Tandem repeats consist in approximate and adjacent repetitions of a DNA motif. Such repeats account for large portions of eukaryotic genomes and have also been found in other life kingdoms. Owing to their polymorphism, tandem repeats have …
Long direct repeats in genomes arise from molecular duplication mechanisms like retrotransposition, copy of genes, exon shuffling, ... Their study in a given sequence reveals its internal repeat structure as well as part of its evolutionary history. …