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). 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 improved 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 and the best known previous algorithm for this problem takes time Ω(|X| log3 |X|).
CITATION STYLE
Muthukrishnan, S., & Ṣahinalp, S. C. (2002). An improved algorithm for sequence comparison with block reversals. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 2286, pp. 319–325). Springer Verlag. https://doi.org/10.1007/3-540-45995-2_30
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