Alienness: rapid detection of candidate horizontal gene transfers across the tree of life - Archive ouverte HAL Accéder directement au contenu
Article Dans Une Revue Genes Année : 2017

Alienness: rapid detection of candidate horizontal gene transfers across the tree of life

Résumé

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.
Fichier principal
Vignette du fichier
2017_Rancurel_Genes_{1A3B987F-7120-4BFC-9C2A-D41703AED930}.pdf (2.68 Mo) Télécharger le fichier
Origine : Accord explicite pour ce dépôt
Loading...

Dates et versions

hal-01609604 , version 1 (03-10-2017)

Licence

Paternité

Identifiants

Citer

Corinne Rancurel, Ludovic Legrand, Etienne Danchin. Alienness: rapid detection of candidate horizontal gene transfers across the tree of life. Genes, 2017, 8 (10), pp.248. ⟨10.3390/genes8100248⟩. ⟨hal-01609604⟩
76 Consultations
85 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More