Sequence similarity measures based on bounded hamming distance.

A growing number of measures of sequence similarity are being based on some underlying notion of relative compressibility. Within this paradigm, similar sequences are expected to share a large number of common substrings, or subsequences, or more complex patterns or motifs , and so on. In this paper, measures of sequence similarity are introduced and studied in which patterns in a pair are considered similar if they coincide up to a preset number of mismatches, that is, within a bounded Hamming distance. It is shown here that for some such measures bounds are achievable that are slightly better than O ( n 2 ) . Preliminary experiments demonstrate the potential applicability to phylogeny and classification of these similarity measures. [ABSTRACT FROM AUTHOR]