Duplication Distance Research Comprehensive Project

Genome sequences mutate and rearrange through the course of evolution. Genome rearrangement is an important and rich area of computational biology, and has many applications, including inferring phylogenetic trees. Some genome rearrangement problems, such as reversal distance [6], [1] and translocation distance [5], have been studied. Reversal distance, for example, measures the number of substring inversions necessary to transform one signed permutation into another. Translocation distance measures the number of substring “cut-paste” operations that are necessary to transform one signed permutation into another. See [7] for a survey of rearrangement problems. However, there remain many genomic rearrangements that are not well understood, and there does not exist a unified genome rearrangement metric that can be used to quantify the similarity of two arbitrary genomes.