Figure 2

Example of search times as a function of available RAM. To simulate searching with various amounts of free memory, we instructed MICA (K = 6) to search chromosome 1 for Bae I sites (ACNNNNGTAYC) using the procedures that would be followed if the indicated amounts of RAM were available. For these measurements, each search was preceded by a large number of extraneous reads, which flushed the main memory of any prior data from the index.