The first widely used algorithm for similarity searching of protein and DNA sequence databases. The program looks for optimal local alignments by scanning the sequence for small matches called “words”. Initially, the scores of segments in which there are multiple word hits are calculated (“init1”). Later, the scores of several segments may be summed to generate an “initn” score. An optimized alignment that includes gaps is shown in the output as “opt”. The sensitivity and speed of the search are inversely related and controlled by the “k-tup” variable, which specifies the size of a “word” (Pearson and Lipman). Also refers to a format for a nucleic acid or protein sequence.