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This article is part of the supplement: Selected articles from the 7th International Symposium on Bioinformatics Research and Applications (ISBRA'11)

Open Access Proceedings

Horizontal gene transfer dynamics and distribution of fitness effects during microbial in silico evolution

Vadim Mozhayskiy and Ilias Tagkopoulos*

Author Affiliations

Department of Computer Science and UC Davis Genome Center, University of California Davis, Davis, California, 95616, USA

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BMC Bioinformatics 2012, 13(Suppl 10):S13  doi:10.1186/1471-2105-13-S10-S13

Published: 25 June 2012

Additional files

Additional file 1:

Evolution rate as a function of the population size. Rate is calculated as an average slope of the maximum fitness increase averaged over 8 independent experiments for each population size of 256, 512, 1024, 2048, 3072 and 4096. Initial random populations evolved in the XOR environment until the maximum fitness is stabilized.

Format: TIF Size: 86KB Download file

Open Data

Additional file 2:

HGT fragment transfer probability and genome integration. (A) Probability density function profile used to select HGT fragment sizes. (B) Incorporation of the HGT-transferred fragment (triplets TN+1 to TN+k) in the regulatory matrix, where only the response pathway (triplet T0) regulation is conserved. The newly acquired fragment can over time rewire and couple to other nodes in the network. Simulations where the imported fragment was randomly rewired to the host genome yielded similar results.

Format: TIF Size: 193KB Download file

Open Data