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Sequence comparison in computational molecular biology is a powerful tool for deriving evolutionary and functional relationships between genes. However, classical alignment algorithms handle only local mutations (i.e., insertions, deletions, and substitutions of nucleotides) and ignore global rearrangements (i.e., inversions and transpositions of long fragments). As a result, applications of sequence alignment in analyzing highly rearranged genomes (i.e., herpes viruses or plant mitochondrial DNA) are very limited and may lead to contradictions in molecular phylogeny studies since different genes give rise to different evolutionary trees. The paper addresses the problem of genome comparison versus classical gene comparison and presents algorithms to analyze rearrangements in genomes evolving by inversions. In the simplest form the problem corresponds to sorting by reversals, that is, sorting of an array using reversals of arbitrary fragments. We describe algorithms to analyze genomes evolving by inversions and discuss applications of these algorithms in molecular evolution.

Sorting by Reversals: Genome Rearrangements in Plant Organelles and Evolutionary History of X Chromosome