title: Robustness assessment of whole bacterial genome segmentations.
abstract: Comparison of closely related bacterial genomes has revealed the presence of highly conserved sequences forming a "backbone" that is interrupted by numerous, less conserved, DNA fragments. Segmentation of bacterial genomes into backbone and variable regions is particularly useful to investigate, among other things, bacterial genome evolution. Several software tools have been designed to compare complete bacterial chromosomes and a few online databases store pre-computed genome comparisons. However, very few statistical methods are available to evaluate the reliability of these software tools and to compare the results obtained with them. To fill this gap, we have developed two local scores to measure the robustness of bacterial genome segmentations. Our method uses a simulation procedure based on random perturbations of the compared genomes. The two scores described in this article provide useful information and are easy to implement, and their interpretation is intuitive. We show that they are suited to discriminate between robust and non-robust segmentations when genome aligners such as MAUVE and MGA are used.
authors: Mathématique, Informatique et Génome, INRA, UR1077, Jouy-en-Josas, France. hugo.devillers@jouy.inra.fr
authors: Hugo
authors: H
authors: Devillers
authors: Hélène
authors: H
authors: Chiapello
authors: Sophie
authors: S
authors: Schbath
authors: Meriem El
authors: ME
authors: Karoui
mesh_terms: D000465:Algorithms; D002138:Calibration; D017124:Conserved Sequence; D004926:Escherichia coli / Q000235:genetics; D014644:Genetic Variation; D016680:Genome, Bacterial; D008957:Models, Genetic; D044224:Pseudomonas syringae / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D013297:Streptococcus pyogenes / Q000235:genetics