PLoS Computational Biology Volume 2 | Issue 8 | AUGUST 2006
- An Integrative Method for Accurate Comparative Genome Mapping
Comparative genomics is an important discipline with applications in evolutionary, genetic, and ge nome rearrangement studies. When comparing genomes, one is usually interested in investigating the relation between the genomic segments to establish their evolutionary origin: are the segments orthologous, and hence inherited from their most recent common ancestor? Are they paralogs, and hence duplicated from an ancestral segment? Did the segments undergo reordering? Were the segments deleted or inserted and—if so—how (insertion sequence, prophage, horizontal gene transfer)?
In this paper, Swidan et al. present MAGIC, a new approach for comparative genome mapping. The main novelty of this approach is the biologically intuitive clustering step, which aims towards both calculating reorder-free segments and identifying orthologous segments. The authors demonstrate MAGIC's robustness, relative to both its initial input and to its parameters' values. MAGIC's scalability is demonstrated by running it on distantly related organisms and on large genomes. In addition, Swidan et al. provide a detailed analysis of the differences between MAGIC and other comparative mapping methods.
Applying MAGIC to several prokaryotic pairs enabled the authors to address the aforementioned questions and to quantitatively study the different evolutionary forces shaping the prokaryotic genome as well as to investigate their breakpoint distribution.