TY - GEN
T1 - Assessing the robustness of complete bacterial genome segmentations
AU - Devillers, Hugo
AU - Chiapello, Hélène
AU - Schbath, Sophie
AU - El Karoui, Meriem
PY - 2010/12/14
Y1 - 2010/12/14
N2 - 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 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 scores presented in this paper are simple to implement and our results show that they allow to discriminate easily between robust and non-robust bacterial genome segmentations when using aligners such as MAUVE and MGA.
AB - 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 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 scores presented in this paper are simple to implement and our results show that they allow to discriminate easily between robust and non-robust bacterial genome segmentations when using aligners such as MAUVE and MGA.
U2 - 10.1007/978-3-642-16181-0_15
DO - 10.1007/978-3-642-16181-0_15
M3 - Conference contribution
AN - SCOPUS:78649979400
SN - 3642161804
SN - 9783642161803
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 173
EP - 187
BT - Comparative Genomics - International Workshop, RECOMB-CG 2010, Proceedings
T2 - International Workshop on Comparative Genomics, RECOMB-CG 2010
Y2 - 9 October 2010 through 11 October 2010
ER -