Mobile genetic elements with the ability to integrate genetic information into 
chromosomes can cause disease over short periods of time and shape genomes over 
eons. These elements can be used for functional genomics, gene transfer and 
human gene therapy. However, their integration-site preferences, which are 
critically important for these uses, are poorly understood. We analyzed the 
insertion sites of several transposons and retroviruses to detect patterns of 
integration that might be useful for prediction of preferred integration sites. 
Initially we found that a mathematical description of DNA-deformability, called 
V(step), could be used to distinguish preferential integration sites for 
Sleeping Beauty (SB) transposons into a particular 100 bp region of a plasmid 
[G. Liu, A. M. Geurts, K. Yae, A. R. Srinivassan, S. C. Fahrenkrug, D. A. 
Largaespada,J. Takeda, K. Horie, W. K. Olson and P. B. Hackett (2005) J. Mol. 
Biol., 346, 161-173 ]. Based on these findings, we extended our examination of 
integration of SB transposons into whole plasmids and chromosomal DNA. To 
accommodate sequences up to 3 Mb for these analyses, we developed an automated 
method, ProTIS, that can generate profiles of predicted integration events. 
However, a similar approach did not reveal any structural pattern of DNA that 
could be used to predict favored integration sites for other transposons as well 
as retroviruses and lentiviruses due to a limitation of available data sets. 
Nonetheless, ProTIS has the utility for predicting likely SB transposon 
integration sites in investigator-selected regions of genomes and our general 
strategy may be useful for other mobile elements once a sufficiently high 
density of sites in a single region are obtained. ProTIS analysis can be useful 
for functional genomic, gene transfer and human gene therapy applications using 
the SB system.