Rancurel, C.; Legrand, L.; Danchin, E.G.J. Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life. Genes2017, 8, 248.
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.
Rancurel, C.; Legrand, L.; Danchin, E.G.J. Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life. Genes2017, 8, 248.
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.
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 metazoan. Here, we propose Alienness, a taxonomy-aware web application that 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 NCBI protein library. The user defines recipient (e.g. metazoan) 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.
Keywords
horizontal gene transfer; alien index; lateral gene transfer
Subject
LIFE SCIENCES, Genetics
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
