An efficient algorithm for sequence comparison with block reversals

Given two sequences X and Y that are strings over some alphabet set, we consider the distance d(X, Y) between them defined to be minimum number of character replacements and block (substring) reversals needed to transform X to Y (or vice versa). The operations are required to be disjoint. This is the “simplest” sequence comparison problem we know of that allows natural block edit operations. Block reversals arise naturally in genomic sequence comparison; they are also of interest in matching music data. We present an algorithm for exactly computing the distance d(X, Y); it takes time O(|X|log2|X|), and hence, is near-linear. Trivial approach takes quadratic time.

Authors

• S. Muthukrishnan
• S. Cenk Sahinalp

Keywords

• Sequence comparison
• Block edit distance
• String periodicity