Merja Oja, Panu Somervuo, Teuvo Kohonen and Samuel Kaski. Clustering of human endogenous retrovirus sequences with median self-organizing map. In Proceedings of the Workshop on Self-Organizing Maps (WSOM'03), Hibikino, Kitakyushu, Japan, September 2003. Proceedings on CD. (postscript, gzipped postscript)

Mutual relationships of human endogenous retroviruses (HERVs) and their similarities to other DNA elements are studied in this paper. We demonstrate that a completely data-driven grouping is able to reflect same kinds of relationships as more traditional biological classifications and phylogenetic taxonomies. The clusters and their visualization were computed with the Median Self-Organizing Map algorithm of pairwise FASTA-based distances. The whole-sequence distances are able to distinguish between the different known types of endogenous elements, and exogenous retroviruses. The HERVs become grouped meaningfully.