Flow diagram of the mathematics of genomic tracks. Genomic tracks are represented as geometric objects on the line defined by the base pairs of the genome sequence: (unmarked (UP) or marked (MP)) points, (unmarked (US) or marked (MS)) segments, and functions (F). The biologist identifies the two tracks to be compared, and the Genomic HyperBrowser detects their type. The biological question of interest is stated in terms of mathematical relations between the types of the two tracks. The relevant questions are proposed by the system. The biologist then selects the question and needs to specify the null hypothesis. For this purpose she is called to decide about what structures are preserved in each track, and how to randomize the rest. Thereafter, the Genomic HyperBrowser identifies the relevant test statistics, and computes actual P-values, either exactly or by Monte Carlo testing. Results are then reported, both for a global analysis, answering the question on the whole genome (or area of study), and for a local analysis. Here, the area is divided into bins, and the answer is given per bin. P-values, test-statistic, and effect sizes are reported, as tables and graphics. Significance is reported when found, after correction for multiple testing.