A considerable time in computational genomics is spent on overlapping different features of the genome. For example, you may want to overlap transcription factor binding sites with CpG islands or promoters to quantify what percentage of binding sites overlap with your regions of interest. Overlapping mapped reads from high-throughput sequencing experiments with genomic features such as exons, promoters, enhancers can also be classfied as operations on genomic intervals. You can think of a million other ways that involves overlapping two sets of different features on the genome. This chapter aims to show how to do analysis involving operations on genomic intervals.