This tool incorporates domain knowledge that has proven to be important in our experimental process. We also formulated a framework for systematically solving a general nucleotide selection problem and produced the program Scan to assist in the selection process. One of SCAN's designs has been implemented in the laboratory and has shown a marked performance improvement over the products of previous attempts at manual design. This design is the one currently under investigation. We are continuing to develop tools and algorithms to provide a greater understanding of the systems we are exploring in the laboratory.
Ongoing work is in two primary directions.
The first is a theoretical exploration of the computational power of various biological computation systems. The second is the development of a more powerful simulation tool, capable of predicting the complete array of DNA strands that are produced during each cycle of a programmed mutagenesis reaction.