Selected combinatorial optimization problems arising in molecular biology

Throughout the last forty years molecular biology, whose aim is to study DNA construction and functioning, has emerged as a clearly defined research area with specific notions and experimental tools. It appeared, however, that massive amounts of data gathered from different sources all over the world and complicated models arising in DNA analysis required support from other research disciplines. This paper is concerned with some problems arising in the area of molecular biology that can take advantage of a combinatorial optimization support. Firstly, a problem of sequencing DNA chains is studied. Sequencing algorithms for the case of negative errors are presented and some open questions are posed. Then, the DNA assembling problem is analyzed. Lastly, the problem of DNA chain alignment is discussed. Prospects of further research are also discussed.