SORTING BY REVERSALS - GENOME REARRANGEMENTS IN PLANT ORGANELLES AND EVOLUTIONARY HISTORY OF X-CHROMOSOME

Sequence comparison in computational molecular biology is a powerful t ool for deriving evolutionary and functional relationships between gen es. However, classical alignment algorithms handle only local mutation s (i.e., insertions, deletions, and substitutions of nucleotides) and ignore global rearrangements (i.e., inversion and transpositions of lo ng fragments). As a result, applications of sequence alignment in anal yzing highly rearranged genomes (i.e., herpes viruses or plant mitocho ndrial DNA) are very limited and may lead to contradictions in molecul ar phylogeny studies since different genes give rise to different evol utionary trees. The paper addresses the problem of genome comparison v ersus classical gene comparison and presents algorithms to analyze rea rrangements in genomes evolving by inversions. In the simplest form th e problem corresponds to sorting by reversals, that is, sorting of an array using reversals of arbitrary fragments. We describe algorithms t o analyze genomes evolving by inversions and discuss applications of t hese algorithms in molecular evolution.