Assessing the quality of whole genome alignments in bacteria

Comparing genomes is an essential preliminary step to solve many problems in biology. Matching long similar segments between two genomes is a precondition for their evolutionary, genetic, and genome rearrangement analyses. Though various comparison methods have been developed in recent years, a quantitative assessment of their performance is lacking. Here, we describe two families of assessment measures whose purpose is to evaluate bacteria-oriented comparison tools. The first measure is based on how well the genome segmentation fits the gene annotation of the studied organisms; the second uses the number of segments created by the segmentation and the percentage of the two genomes that are conserved. The effectiveness of the two measures is demonstrated by applying them to the results of genome comparison tools obtained on 41 pairs of bacterial species. Despite the difference in the nature of the two types of measurements, both show consistent results, providing insights into the subtle differences between the mapping tools.