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Open Access Research article

Detection of horizontal transfer of individual genes by anomalous oligomer frequencies

Jeff Elhai1*, Hailan Liu2 and Arnaud Taton13

Author Affiliations

1 Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA

2 Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou,, Zhejiang 310058, China

3 Division of Biological Sciences, University of California San Diego, La Jolla, San Diego, CA, 92093, USA

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BMC Genomics 2012, 13:245  doi:10.1186/1471-2164-13-245

Published: 15 June 2012

Additional files

Additional file 1:

Support for phylogenetic tree inferred from 16 S rRNA gene sequences [26,59-64].

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Additional file 2:

Experimental results summarized in this work.

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Additional file 3:

CGS scores of genes.

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Additional file 4:

Genomes with contaminated cores, seeded with genes from other genomes.

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Additional file 5:

Comparison of CGS method using one strand or both strands of genome.

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Additional file 6:

Comparison of CGS method using hexamer or octamer frequencies.

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Additional file 7:

Comparison of covariance and G-score methods.

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Additional file 8:

Influence of size of reference set on maximal discrimination.

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Additional file 9:

Putative foreign gene summary in genomes without artificial contamination by foreign genes.

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Additional file 10:

Phylogenetic trees of conserved genes with reported conflicts.

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Additional file 11:

Fraction of genes identified as putative foreign by different methods compared to CGS.

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Additional file 12:

Evolutionary context of genes of Synechocystis PCC 6803.

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