Section: Scientific Foundations
Combinatorial discrete models and algorithms
Our research is driven by biological questions. At the same time, we have in mind to develop well-founded models and efficient algorithms. Biological macromolecules are naturally modelled by various types of discrete structures: String, trees, and graphs. String algorithms is an established research subject of the team. We have been working on spaced seed techniques for several years  ,  ,  ,  ,  . Members of the team have also a strong expertise in text indexing and compressed index data structures  ,  ,  . Such methods are widely-used for the analysis of biological sequences because they allow a data set to be stored and queried efficiently. Ordered trees and graphs naturally arise when dealing with structures of molecules, such as RNAs  ,  ,  ,  ,  or non-ribosomal peptides  . The underlying questions are: how to compare molecules at structural level, how to search for structural patterns ? String, trees and graphs are also useful to study genomic rearrangements: Neighborhoods of genes can be modelled by oriented graphs, genomes as permutations, strings or trees.