Effect of alphabet reduction on the running time of ESAsearch. Experiment 6: Relative deviations of running time of ESAsearch when using reduced alphabets at different levels of stringency. We measured the relative percentage deviation with respect to the running time when using the standard 20 letter amino acid alphabet (= 0%). We searched with 11,411 PSSMs from the PRINTS database (Rel. 38) in the RCSB Protein Data Bank (PDB) with a total sequence length of 4.3 MB. In this example, the maximum performance improvement is achieved for an alphabet of size 4 and a p-value cutoff of π = 10-20.