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Section: Research Program

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 also have a strong expertise in text indexing and compressed index data structures, such as BWT. 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. High-performance computing is another tool that we use to achieve our goals.