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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 [20] , [27] , [29] , [23] , [22] . Members of the team have also a strong expertise in text indexing and compressed index data structures  [28] , [31] , [30] . 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  [32] , [26] , [25] , [24] , [17] or non-ribosomal peptides [18] . 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.