Radoje T. Drmanac

Simulations of ordering and sequence reconstruction of random DNA clones hybridized with a small number of oligomeric probes

The sequencing by hybridization (SBH) method has been developed for assaying millions of 0.5 to 2-kb-long clones. This opens up an efficient way for defining the order of short clones and creating a physical map at 100-bp resolution. Moreover, complete sequences can be obtained using a modest number (about 3,000) of probes if hybridization and gel sequence data from overlapped or similar sequences are used. In light of these possibilities, various heuristic algorithms have been developed and tested in simulation experiments. This approach can influence the interpretation of the intuitively obvious term, ``known sequence.``