A computational method that uses protein structures to detect horizontal gene transfer

No current method to detect Horizontal Gene Transfer (HGT) events between organisms is accurate in all cases. This paper presents a novel computational method that uses protein structures to detect HGT. The use of protein structures instead of protein sequences increases the accuracy of our method. The new method uses Z-score similarities between the protein structures and DaliLite to search efficiently for similarities in both protein sequences and structures. In addition, the Java viewer tool Jmol is used for visual structural comparisons and sequence alignment. The experimental results include six previously unreported cases of HGTs between various Firmicutes and Proteobacteria bacteria. Various methods of handling false positives are also described.