We present a novel approach to comparing saccadic eye movement sequences based on the Needleman-Wunsch algorithm used in bioinformatics to compare DNA sequences. In the proposed method, the saccade sequence is spatially and temporally binned and then recoded to create a sequence of letters that retains fixation location, time, and order information. The comparison of two letter sequences is made by maximizing the similarity score computed from a substitution matrix that provides the score for all letter pair substitutions and a penalty gap. The substitution matrix provides a meaningful link between each location coded by the individual letters. This link could be distance but could also encode any useful dimension, including perceptual or semantic space. We show, by using synthetic and behavioral data, the benefits of this method over existing methods. The ScanMatch toolbox for MATLAB is freely available online (www.scanmatch.co.uk). © 2010 The Psychonomic Society, Inc.