Section: Overall Objectives
The main goal of Sequoia project-team is to define appropriate combinatorial models and efficient algorithms for large-scale sequence analysis in molecular biology. An emphasis is made on the annotation of non-coding regions in genomes – RNA genes and regulatory sequences – via comparative genomics methods. This task involves several complementary issues such as sequence comparison, prediction, analysis and manipulation of RNA secondary structures, identification and processing of regulatory sequences. Efficient algorithms and parallelism on high-performance computing architectures allow large-scale instances of such issues. Our aim is to tackle all those issues in an integrated fashion and to put together the developed software tools into a common platform for annotation of non-coding regions. We also explore complementary problems of protein sequence analysis. Those include new approaches to protein sequence comparison on the one hand, and a system for storing and manipulating nonribosomal peptides on the other hand. A special attention is given to the development of robust software, its validation on biological data and to its availability from the software platform of the team and by other means. Most of research projects are carried out in collaboration with biologists.