Genome Rearrangement
نویسندگان
چکیده
The difference between genome rearrangement theory and other approaches to comparative genomics, and indeed most other topics in computational molecular biology, is that it is not directly based on macromolecular sequences, either nucleic acids or proteins. Rather like classical genetics, its building blocks are genes, and the structures of interest are chromosomes, abstracted in terms of the linear order of the genes they contain. Of course genes and their RNA and protein products are macromolecules, but here we do not focus on the internal structure of genes and assume that the problems of determining the identity of each gene, and its homologs in other genomes, have been solved, so that a gene is simply labeled by a symbol indicating the class of orthologs to which it belongs. Moreover, the linearity of chromosomal structure does not evolve by a nucleotide substitution process in the way DNA does, or even by the same type of insertion/deletion processes, but by a number of very different rearrangement processes which are non-local, i.e. their scope may involve an arbitrarily large proportion of a chromosome. As a consequence, the formal analysis of rearrangements bears little resemblance in detail to DNA or protein comparison algorithms. Nevertheless, in analogy with sequence comparison, the study of genome rearrangements has focused on inferring the most economical explanation for observed differences in gene orders in two or more species, as represented by their genomes, in terms of a small number of elementary processes. After first formalizing in Section 2 the notion of a genome as a set of chromosomes, each consisting of an ordered set of genes, we will proceed in Section 3 to a survey of genomic distance problems. More detail on the Hannehanlli-Pevzner theory for “signed” distances follows in Section 4. Section 5 will be devoted to phylogenetic extensions, and Section 6 to problems of gene and genome duplication and their implications for genomic distance and genome-based phylogeny.
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