For millions of years, L1 retrotransposons have been duplicating in mammalian genomes by an efficient "copy and paste" mechanism; consequently, L1s now make up 15% of the human genome. These autonomous elements are thought to have played an important role in the expansion and evolution of our genome. For example, a recent, and still active, L1 element was found to have inserted into genes, thereby causing disease. We show examples of 3' transduction events for this particular L1, which represents another mechanism by which L1s have probably shaped the human genome. Part of the preparation for this project involves a complete analysis of the L1 elements in the human genome sequence. Of particular interest has been the development of an improved algorithm for the identification of the target-site duplications that flank the L1 insertion sequences. In addition, a complete analysis of the human genome sequence has been performed to identify all copies of families of processed pseudogenes. Several families of HMG (high mobility group) genes cDNA products were used to identify all the processed pseudogenes of 8 classes of HMG genes. By comparison of the processed pseudogene sequences to the database of ESTs (dbEST) we also identified several candidate pseudogenes which could be expressed. These would therefore be classified as intronless paralogs rather than processed pseudogenes.