A guide to simulation (2nd ed.)
A guide to simulation (2nd ed.)
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
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With the increase of the number of available prokaryotic genomes, studies focusing on the higher level evolutionary events, including the evolution of whole genomes, are now possible. Simulated datasets are essential components in both the development and evaluation stages for all evolutionary studies. In this paper, we implemented the first random events-based high level bacterial genome evolution simulator with models for a large number of possible events at both the gene- and replicon-scale. We call this simulator Prokaryote Evolutionary Genomics Simulator (PEGsim). PEGsim also implements the concept of conserved blocks, which can be biologically related to both Operons and/or regulons. We present results showing genome sizes and replicon numbers in simulated data and in real data. These results demonstrate that PEGsim is capable of generating evolutionary-related bacterial genome datasets with diverse realistic properties.