Multiple genome rearrangements

Multiple alignment of macromolecular sequences, an important topic of algorithmic research for at least 25 years 113, lo], generalizes the compsrison of just two sequences which have diverged through the local processes of insertion, deletion and substitution. Recently there has been much interest in gene-order sequences which diverge through non-local genome rearrangement processes such as inversion (or reversal) and transposition (reviewed in [15] ch.7, [9], [S] ch. 19 and 131). What would be the analog of multiple alignment under these models of divergence? In this introduction we tit review some formulations of multiple alignment and show which have counterparts in multiple rearrangement. We then discuss the difiiculties inherent in edit-distance formulations of multiple rearrangement, referring to relevant work, and argue for a potentially simpler approach based on “breakpoint analysis”.