The early personal computers had insufficient memory and were too slow to carry out a database scan using dynamic programming.
Speed is achieved by employing a look up procedure.
Sequence is scanned once and the location of each -tuple in is recorded in the corresponding element of . Sequence is then scanned and by reference to the location of all -tuple matches common to and may be identified. The region giving the highest score for the protein comparison was used to rank order the sequences located in the databank for further study by more rigorous procedures. If there are several initial regions above a pre set cutoff score then those that could form a longer alignment are joined, allowing for gaps and a score initn is calculated by subtracting a penalty for each gap. Finally, dynamic programming is used over a narrow region of the high scoring diagonal to produce an alignment with score opt .