An Efficient Algorithm for the Detection and Classification of Horizontal Gene Transfer Events and Identification of Mosaic Genes

In this article we present a new algorithm for detecting partial and complete horizontal gene transfer (HGT) events which may give rise to the formation of mosaic genes. The algorithm uses a sliding window procedure that analyses sequence fragments along a given multiple sequence alignment (MSA). The size of the sliding window changes during the scanning process to better identify the blocks of transferred sequences. A bootstrap validation procedure incorporated in the algorithm is used to assess the bootstrap support of each predicted partial or complete HGT. The proposed technique can be also used to refine the results obtained by any traditional algorithm for inferring complete HGTs, and thus to classify the detected gene transfers as partial or complete. The new algorithm will be applied to study the evolution of the gene rpl12e as well as the evolution of a complete set of 53 archaeal MSA (i.e., 53 different ribosomal proteins) originally considered in [13].