RT Journal Article
SR Electronic
T1 HGTector: An automated method facilitating genome-wide discovery of putative horizontal gene transfers
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 003731
DO 10.1101/003731
A1 Qiyun Zhu
A1 Michael Kosoy
A1 Katharina Dittmar
YR 2014
UL http://biorxiv.org/content/early/2014/04/02/003731.abstract
AB 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 further tested on real genomic datasets, including Rickettsia genomes, and was compared to previous studies. Results show consistency with currently employed categories of HGT prediction methods. In-depth analysis of both simulated and real genomic data suggests that the method is notably insensitive to stochastic events such as gene loss, rate variation and database error, which are common challenges to the current methodology. An automated pipeline was created to implement this approach and was made publicly available at: https://github.com/DittmarLab/HGTector. The program is versatile, easily deployed, has low requirements for computational resources, and is an effective tool for initial or standalone large-scale discovery of candidate HGT-derived genes.