Aligning two fragmented sequences

Upon completion of the human and mouse genome sequences, world-wide sequencing capacity will turn to other complex organisms. Current strategies call for many of these genomes to be incompletely sequenced. That is, holes will remain in the known sequence, and the relative order and orientation of the known sequence fragments may not be determined. Sequence comparison between two genomes of this sort may allow some of the fragments to be oriented and ordered relative to each other by computational means. We formalize this as an optimization problem, show that the problem is MAX-SNP hard, and develop a polynomial time algorithm that is guaranteed to produce a solution whose score is within a factor 3 of optimal.