Contig Ordering Based on Physical Subunit Orders of ATP Synthase

Ordering contigs obtained from random shotgun sequencing approach could be a problematic and laborious work. Other than simply extending coverage (10X or higher), various strategies have been suggested such as split peptides, oligonucleotide finger print comparisons, combinatorial reactions with all contig end-oligonucleotides, dye terminator reactions and so on. But we could also order contigs of a target organism based on the clustering information of protein subunits in other organisms. We downloaded the gene listings of 30 organisms whose whole genome sequences have been published. Then we studied the patterns of subunits of ATP synthase of these organisms and applied this information to order contigs of Haemophilus influenzae, our sample organism.