Speed comparisons for localized and chromosome-wide alignments. 1000 randomly selected mouse mRNAs are aligned against the human genome. In the localized plot, every data point represents the average of 50 alignments. In chromosome-wide plot, every data point is a single chromosome. This plot is limited to CAT, BLAT, and sim4 because they are the only ones that run in a reasonable amount of time and/or memory.