Section: Scientific Foundations

Combinatorial optimization

For wide genome analysis, Next Generation Sequencing (NGS) data processing or protein structure applications, the main issue concerns the exploration of sets of data by time-consuming algorithms, with the aim of identifying solutions that are optimal in a predefined sense. In this context, speeding up such algorithms requires acting on many directions: (1) optimizing the search with efficient heuristics and advanced combinatorial optimization techniques [2] , [5] or (2) targeting biological sub-problems to reduce the search space [7] , [9] . Designing algorithms with adapted heuristics, and able to scale from protein (a few hundreds of amino acids) to full genome (millions to billions of nucleotides) is one of the competitive challenges addressed in the GenScale project.