Aug 28, 2014

HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers

BMC Genomics
Qiyun ZhuKatharina Dittmar

Abstract

First pass methods based on BLAST match are commonly used as an initial step to separate the different phylogenetic histories of genes in microbial genomes, and target putative horizontal gene transfer (HGT) events. This will continue to be necessary given the rapid growth of genomic data and the technical difficulties in conducting large-scale explicit phylogenetic analyses. However, these methods often produce misleading results due to their inability to resolve indirect phylogenetic links and their vulnerability to stochastic events. A new computational method of rapid, exhaustive and genome-wide detection of HGT was developed, featuring the systematic analysis of BLAST hit distribution patterns in the context of a priori defined hierarchical evolutionary categories. Genes that fall beyond a series of statistically determined thresholds are identified as not adhering to the typical vertical history of the organisms in question, but instead having a putative horizontal origin. Tests on simulated genomic data suggest that this approach effectively targets atypically distributed genes that are highly likely to be HGT-derived, and exhibits robust performance compared to conventional BLAST-based approaches. This method was furthe...Continue Reading

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Mentioned in this Paper

In Silico
Rickettsia
Acropectoral Syndrome
Genome
Computer Programs and Programming
Gene Transfer, Horizontal
Genomics
Genes, Bacterial
Recombination, Interspecies
Genome, Microbial

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