Successful DNA differential methylation screening by unbiased fingerprinting-like techniques such as amplification of intermethylated sites (AIMS) is ensured by state-of-the art bioinformatic approaches providing virtual imaging. As an instrument for designing AIMS experiments by preliminary modeling of expected results in silico, we have developed an AIMS in silico computer program. This program predicts the total number of the PCR products obtainable with AIMS with preset conditions, the distribution of the products by their lengths, and their individual sequences. Graphical information is presented as a virtual capillary electrophoregram. Our AIMS in silico 2.0 version also allows virtual restriction analysis of the AIMS products, assisting in validation of the DNA fragments mapping to the genome. In an original AIMS approach, radioactively labeled DNA fragments are visualized with slab gels exposed on X-ray films. We have chosen to improve the method by separation of the AIMS products by capillary electrophoresis; thus, the results are witnessed as the sets of peaks of the capillary electrophoregram. In order to view the raw data and to perform exact sizing and comparative analysis of the DNA fragments, we have developed the PeakPick computer program. The necessity for this product is explained by inhability of the existing commercial software to analyze complex fingerprint-like capillary electrophoregrams, where the adjacent peaks tend to influence each other distorting the landscape. PeakPick provides very delicate but thorough processing in order to achieve exact sizing and to preserve true peak shapes, amplitudes, and squares. This allows high quality correlation and differentiation of capillary electrophoregrams in order to highlight methylation differences. PeakPick software, as well as the AIMS in silico program, may in principle be applicable to other fingerprint-like laboratory techniques, such as amplified fragment length polymorphism (AFLP) or a recently proposed amplification of unmethylated Alu’s (AUMA). The programs are freely available at http://abif.freeflux.net. This research was supported by Friends for an Earlier Breast Cancer Test (USA); Russian Foundation for Basic Research (grant 08-04-01685-а); and by the Federal Target Program “Scientific and scientific-educational personnel of innovation Russia” of the Federal Science and Innovations Agency (Rosnauka), contract no. 02.740.11.0089. INTEGRATED ANALYSIS OF DNA COPY NUMBER ALTERATIONS AND GENE EXPRESSION MICROARRAY DATA OF UTERINE LEIOMYOMAS