SOFTWARE AND WEB TOOLS
webMGR: An Online Tool for the Multiple Genome Rearrangement Problem
The algorithm MGR enables the reconstruction of rearrangement phylogenies based on gene or synteny block order in multiple genomes. Although MGR has been successfully applied to study the evolution of different sets of species, its application has been hampered by the prohibitive running time for some problems. In the current work, we have designed new heuristics that significantly speed up the tool without compromising its accuracy. Furthermore, we have developed a web server (webMGR) that includes elaborate web output to facilitate navigation through the results.
Journal Paper: C.H. Lin, H. Zhao, S.H. Lowcay, A. Shahab, G. Bourque. 2009. webMGR: An Online Tool for the Multiple Genome Rearrangement Problem. Submitted. PubMed
Efficient Method to Recover Ancestral Events (EMRAE)
The analysis of genome rearrangements provides a global view on the evolution of a set of related species. We present
a new algorithm called EMRAE (efficient method to recover ancestral events) to reliably predict a wide-range of rearrangement
events in the ancestry of a group of species. Using simulated data sets, we show that EMRAE achieves comparable
sensitivity but significantly higher specificity when predicting evolutionary events relative to other tools to study
email.
Journal Paper: H. Zhao, G. Bourque. 2009. Recovering Genome Rearrangements in the Mammalian Phylogeny.Genome Res. 19: 934-942. PubMed
Multipe Genome Rearrangements (MGR)
Recent progress in genome-scale sequencing and comparative mapping raises new challenges in studies of genome rearrangements. Although the pairwise genome rearrangement problem is well-studied, algorithms for reconstructing rearrangement scenarios for multiple species are in great need. The previous approaches to multiple genome rearrangement problem were largely based on the breakpoint distance rather than on a more biologically accurate rearrangement (reversal) distance. Another shortcoming of the existing software tools is their inability to analyze rearrangements (inversions, translocations, fusions, and fissions) of multichromosomal genomes. This paper proposes a new multiple genome rearrangement algorithm that is based on the rearrangement (rather than breakpoint) distance and that is applicable to both unichromosomal and multichromosomal genomes. We further apply this algorithm for genome-scale phylogenetic tree reconstruction and deriving ancestral gene orders. In particular, our analysis suggests a new improved rearrangement scenario for a very difficult Campanulaceae cpDNA dataset and a putative rearrangement scenario for human, mouse and cat genomes.
Journal Paper: G. Bourque and P. Pevzner. 2002. Genome-Scale Evolution: Reconstructing Gene Orders in the Ancestral Species. Genome Res. 12(1): 26–36. PubMed