Franco Preparata and Eliezer Upfal are attempting to make improvements to a lesser-used method known as sequencing by hybridization. In their method, they insert gaps that act as wildcards in DNA probes. The DNA to be sequenced binds to some of the probes on a tiny glass chip called a microarray. Then the DNA can be detected and read. Using the information obtained from the probes on the microarray, a computer program is then used to construct the long sequence of bases in the target DNA strand.
Current techniques can construct only a few hundred bases.
Instead of a few hundred bases, you could do tens of thousands. Based on a novel mathematical insight, Preparata and Upfal have designed a new pattern for the probes on the chip. In the new pattern, some of the DNA bases in each probe are replaced by gaps that act like wildcards. The new design extracts substantially more information about the DNA than previously designed probes. Together with the new probe design, they have also developed a new algorithm, tailored to the new probe pattern, that uses the information obtained from the probes to reconstruct the original sequence.