We consider four important combinatorial problems that arise in computa- tional biology and show how they can be modeled as integer programming problems. These models are then solved using branch-and-bound algorithms. Computational experi- ments using real and simulated data are performed and the effectiveness of the algorithms is analyzed. In this paper we study four string selection problems that arise in computational biology applications. We show how to model these problems using Integer Programming (IP) and we carry out computational experiments using these models. The experimental results show the effectiveness of IP techniques for solving problems in computational biology. For all tested instances, it was possible to solve them to optimality in a few minutes in a personal computer. In section 2 we dene the problems studied and in section 3 we introduce notation. In section 4 we formulate each problem described in section 2 using integer programming. In section 5 we present computational experiments over real and simulated instances. Finally, in section 6 conclusion remarks are given.
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