Rearrangements of DNA sequences and SBH

Despite recent advances in DNA sequencing by hybridization it is still a random shotgun method. Even if one manages to routinely sequence short DNA fragments by SBH these fragments have to be assembled into the final genomic sequence. Recently different additional biochemical experiments were suggested which potentially may drastically increase the resolving power of SBH. However biologists frequently cannot estimate the computer science limitations of the proposed additional experiments and no computational studies of additional experiments for SBH were provided yet. The paper discusses a combinatorial technique which might help a biologist to analyze different additional biochemical experiments and to combine these data with SBH data to increase the resolving power of SBH.