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Detecting Laterally Transferred Genes

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Evolutionary Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 855))

Abstract

Methods for identifying alien genes in genomes fall into two general classes. Phylogenetic methods examine the distribution of a gene’s homologues among genomes to find those with relationships not consistent with vertical inheritance. These approaches include identifying orphan genes which lack homologues in closely related genomes and genes with unduly high levels of similarity to genes in otherwise unrelated genomes. Rigorous statistical tests are available to place confidence intervals for predicted alien genes. Parametric methods examine the compositional properties of genes within a genome to find those with atypical properties, likely indicating the directional mutational pressures of a donor genome. These methods may compare the properties of genes to genomic averages, properties of genes to each other, or properties of large, multigene regions of the chromosome. Here, we discuss the strengths and weaknesses of each approach.

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Acknowledgments

This work was supported by NIH grant GM078092.

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Authors and Affiliations

  1. Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA

    Rajeev K. Azad & Jeffrey G. Lawrence

  2. Departments of Biological Sciences and Mathematics, University of North Texas, Denton, TX, USA

    Rajeev K. Azad

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  1. Rajeev K. Azad
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  2. Jeffrey G. Lawrence
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Correspondence to Jeffrey G. Lawrence .

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  1. Department of Computer Science, ETH Zürich, Universitätsstr. 6, Zürich, 8092, Switzerland

    Maria Anisimova

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Azad, R.K., Lawrence, J.G. (2012). Detecting Laterally Transferred Genes. In: Anisimova, M. (eds) Evolutionary Genomics. Methods in Molecular Biology, vol 855. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-582-4_10

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  • DOI: https://doi.org/10.1007/978-1-61779-582-4_10

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