DarkHorse: a method for genome-wide prediction of horizontal gene transfer
Scripps Genome Center, Scripps Institution of Oceanography, University of California at San Diego, Gilman Drive, La Jolla, CA 92093-0202, USA
Genome Biology 2007, 8:R16 doi:10.1186/gb-2007-8-2-r16Published: 2 February 2007
A new approach to rapid, genome-wide identification and ranking of horizontal transfer candidate proteins is presented. The method is quantitative, reproducible, and computationally undemanding. It can be combined with genomic signature and/or phylogenetic tree-building procedures to improve accuracy and efficiency. The method is also useful for retrospective assessments of horizontal transfer prediction reliability, recognizing orthologous sequences that may have been previously overlooked or unavailable. These features are demonstrated in bacterial, archaeal, and eukaryotic examples.