Singh The goal of this project is to construct an attached processor using application specific integrated circuits. This processor will perform high speed partial pattern matching of biological sequence data (such as DNA or protein sequences) against entries in a database. This processor will serve as a filter to provide information on partial matches (of segments) at a very high speed. This partial match information is used by the host processor to determine which sequences merit further detailed comparison (i.e., this prefiltering greatly limits the number of sequences which must be subsequently compared when considering insertions and deletions of subsequences). The subsequent full match will be carried out in the host processor.
