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Genes 2017, 8(10), 248; doi:10.3390/genes8100248

Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life

1
INRA, CNRS, ISA, Université Côte d’Azur, 06903 Sophia Antipolis Cedex, France
2
LIPM, INRA, CNRS, Université de Toulouse, 31326 Castanet-Tolosan Cedex, France
*
Author to whom correspondence should be addressed.
Received: 31 August 2017 / Revised: 22 September 2017 / Accepted: 22 September 2017 / Published: 29 September 2017
(This article belongs to the Special Issue Horizontal Gene Transfer)
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Abstract

Horizontal gene transfer (HGT) is the transmission of genes between organisms by other means than parental to offspring inheritance. While it is prevalent in prokaryotes, HGT is less frequent in eukaryotes and particularly in Metazoa. Here, we propose Alienness, a taxonomy-aware web application available at http://alienness.sophia.inra.fr. Alienness parses BLAST results against public libraries to rapidly identify candidate HGT in any genome of interest. Alienness takes as input the result of a BLAST of a whole proteome of interest against any National Center for Biotechnology Information (NCBI) protein library. The user defines recipient (e.g., Metazoa) and donor (e.g., bacteria, fungi) branches of interest in the NCBI taxonomy. Based on the best BLAST E-values of candidate donor and recipient taxa, Alienness calculates an Alien Index (AI) for each query protein. An AI > 0 indicates a better hit to candidate donor than recipient taxa and a possible HGT. Higher AI represent higher gap of E-values between candidate donor and recipient and a more likely HGT. We confirmed the accuracy of Alienness on phylogenetically confirmed HGT of non-metazoan origin in plant-parasitic nematodes. Alienness scans whole proteomes to rapidly identify possible HGT in any species of interest and thus fosters exploration of HGT more easily and largely across the tree of life. View Full-Text
Keywords: horizontal gene transfer; alien index; lateral gene transfer horizontal gene transfer; alien index; lateral gene transfer
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Rancurel, C.; Legrand, L.; Danchin, E.G.J. Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life. Genes 2017, 8, 248.

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