Section: Overall Objectives
Bonsai is an interdisciplinary project whose scientific core is the design of efficient algorithms for the analysis of biological macromolecules.
From a historical perspective, research in bioinformatics started with string algorithms designed for the comparison of sequences. Bioinformatics became then more diversified and by analogy to the living cell itself, it is now composed of a variety of dynamically interacting components forming a large network of knowledge: Systems biology, proteomics, text mining, phylogeny, structural biology, etc. Sequence analysis still remains a central node in this interconnected network, and it is the heart of the Bonsai team.
It is a common knowledge nowadays that the amount of sequence data available in public databanks grows at an exponential pace. Conventional DNA sequencing technologies developed in the 70's already permitted the completion of hundreds of genome projects that range from bacteria to complex vertebrates. This phenomenon is dramatically amplified by the recent advent of Next Generation Sequencing (NGS), that gives rise to many new challenging problems in computational biology due to the size and the nature of raw data produced. The completion of sequencing projects in the past few years also teaches us that the functioning of the genome is more complex than expected. Originally, genome annotation was mostly driven by protein-coding gene prediction. It is now widely recognized that non-coding DNA plays a major role in many regulatory processes. At a higher level, genome organization is also a source of complexity and have a high impact on the course of evolution.
All these biological phenomena together with big volumes of new sequence data provide a number of new challenges to bioinformatics, both on modeling the underlying biological mechanisms and on efficiently treating the data. This is what we want to achieve in Bonsai . For that, we have in mind to develop well-founded models and efficient algorithms. Biological macromolecules are naturally modeled 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 modeled by oriented graphs, genomes as permutations, strings or trees.
A last point worth mentioning concerns the dissemination of our work to the biology and health scientific community. Since our research is driven by biological questions, most of our projects are carried out in collaboration with biologists. A special attention is given to the development of robust software, its validation on biological data and its availability from the software platform of the team: http://bioinfo.lille.inria.fr/.