Section: Overall Objectives

Overall Objectives

The project-team Adage was created on January 1, 2001, as a result of the evolution of the Polka project-team. The general goal of Adage is to develop efficient algorithms on discrete structures (such as words, trees, polyominoes, ...). This goal leads us to study in depth mathematical properties of those structures, that can be of combinatorial or probabilistic nature.

One of our research directions is word combinatorics and sequence algorithms . Here, we work on the complexity analysis of problems on words (texts, or symbolic sequences) and on the development of efficient algorithms on words. Another research direction belongs to the area of discrete geometry . The structures studied here are discrete geometric objects, described by sets of points in or . As in the previous case, our goal is to develop efficient algorithms that either verify some properties or that compute some geometric parameters of those structures.

Often, we need to study our models from a probabilistic point of view in order to estimate their ``typical'' properties or their accuracy on typical data. We then get interested in a probabilistic analysis of the underlying model.

One application area of our models and algorithms is of a particular importance to us: this is computational biology, where discrete models come up in a very natural and essential way. Here, we are carrying out a number of projects on DNA sequence analysis. Those problems essentially use biological knowledge and are mostly done in collaboration with biologists.

We pay a special attention to implementing our algorithms into experimental software systems and to making them available to the scientific community. Two deliverable DNA sequence analysis programs have been developed by our team: the first one, called mreps , allows to compute all tandem repeats in a given DNA sequence; another one, called YASS , computes all similarity regions between two genomic sequences or within a single one. Another sequence analysis software, named grappe , was developed earlier. Finally, several software programs ( SIGffRid , RepCluster ) are currently under development (see the software section below).

The year 2005 has been of a particular importance for Adage . On the one hand, it is the last year of the existence of the team. Due to the leave of two of its members, including the team leader, Adage will give rise to a new team in 2006. On the other hand, Adage was evaluated on March 31 - April 1, 2005, at the INRIA evaluation seminar for the BIO program. The evaluation of our work during 2001-2004 proved to be positive in the whole. The obtained results, both their originality and significance, have been appreciated by the experts. Even more important, the whole methodological approach of Adage has been approved. We therefore consider this evaluation to be a successful conclusion of the work of Adage .