Table 3.

Run time for amino acid locate() and count() functions

Amino acid search		Count() Time (s)			Locate() Time (s)
Query length	Hits/query	SeqAn3	AWFM	Speed-up	SeqAn3	AWFM	Speed-up
10	1.00	4.58	.81	5.66	6.40	1.63	3.92
9	1.00	3.91	.83	4.71	5.97	1.38	4.33
8	1.02	3.39	.60	5.69	5.29	1.46	3.61
7	1.47	2.89	.43	6.77	5.41	1.61	3.36
6	9.00	2.38	.38	6.27	15.35	5.52	2.78
5	137.70	1.81	.08	21.95	167.56	73.42	2.28
4	2339.23	0.49	0.30	1.62	1950.45	904.28	2.16

A 200 million character-long simulated target amino acid sequence was indexed with a suffix array sampling ratio of 4. One million length-k amino acid query sequences were sampled from the target, for several values of k