Greedy algorithms for optimized DNA sequencing

We discuss the problem of optimally “finishing” a partially sequenced segment of DNA strand. While a simplified model may be solved to optimality by a greedy algorithm, adding more realistic features appears to make the problem computationally hard. We propose an Integer Linear Programming formulation that places it in the context of more general coverage problems, in the hope that this will provide further insight into the solvability of this biologically important application. project’s ambitious timetable, this problem does not ap pear to have been addressed yet in the literature.