An Algorithm for Computing DNA Walks

The process of reading a DNA molecule can be divided into three phases: sequencing, assembly and finishing. The draft sequence after assembly has gaps with no coverage and regions of poor coverage. Finishing by walks is a process by which the DNA in these regions is resequenced. Selective sequencing is expensive and time consuming. Therefore, the laboratory process of finishing is modeled as an optimization problem aimed at minimizing laboratory cost, We give an algorithm that solves this problem optimally and runs in worst case O(n(1 3/4)) time.