Comparison of AnnotateGenomicRegions and BEDTools. AnnotateGenomicRegions and BEDTools were used to annotate identical query regions with identical annotation files. The number of query regions was varied between 10 and 500,000. The response times for AnnotateGenomicRegions were found to be two times faster for up to 100 query regions. For 500,000 query regions, AnnotateGenomicRegions was found to be 30 times faster for 1 annotation (A) and 80 times faster for 10 annotations (B). The tests were performed on an Ubuntu Server Linux computer with 12 CPU's and 16 GB RAM.