On some optimization problems in molecular biology

Abstract

In the last two decades, the study of gene structure and function and molecular genetics have become some of the most prominent sub-fields of molecular biology. Computational molecular biology has emerged as one of the most exciting interdisciplinary fields, riding on the success of the ongoing Human Genome Project, which culminated in the 2001 announcement of the complete sequencing of the human genome. The field has currently benefited from concepts and theoretical results obtained by different scientific research communities, including genetics, biochemistry, and computer science. It is only in the past few years that it has been shown that a large number of molecular biology problems can be formulated as combinatorial optimization problems, including sequence alignment problems, genome rearrangement problems, string selection and comparison problems, and protein structure prediction and recognition. This paper provides a detailed description of some among the most interesting molecular biology problems that can be formulated as combinatorial optimization problems and proposes a new heuristic to find improved solutions for a particular class of them, known as the far from most string problem.