Edit distance for genome comparison based on non-local operations
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TL;DR
A number of measures of gene order rearrangement are defined, algorithm design and software development for the calculation of some of these quantities in single-chromosome genomes are described, and the results of applying these tools to a database of mitochondrial gene orders inferred from genomic sequences are reported on.
Abstract
Detailed knowledge of gene maps and and even complete nucleotide sequences for small genomes has led to the feasibility of evolutionary inference based on the macrostructure of entire genomes, rather than on the traditional comparison of homologous versions of a single gene in different organisms. In this paper, we define a number of measures of gene order rearrangement, describe algorithm design and software development for the calculation of some of these quantities in single-chromosome genomes, and report on the the results of applying these tools to a database of mitochondrial gene orders inferred from genomic sequences.