Table 2.

Sensitivity comparison of databases

Budget	Fugu						Mouse HHAs			Pig HHAs
	HHAs			Exons
	H	S	T	H	S	T	H	S	T	H	C	S	T
w = 10
1	57	58	61	54	56	65	2771	3151	3298	7166	8651	8709	8709
1.5	–	–	69	–	–	71	–	–	3473	–	–	–	8715
2	64	63	71	64	64	74	3045	3450	3528	7361	8721	8751	8749
3	69	69	72	69	70	75	3140	3573	3630	7439	8748	8760	8761
5	71	71	72	70	72	77	3262	3661	3691	7499	8765	8771	8772
7	71	71	72	72	75	77	3303	3708	3719	7520	8771	8778	8775
10	72	72	72	74	76	77	3328	3727	3735	7554	8775	8789	8790
w = 11
1	48	49	56	48	47	58	2522	2909	3062	6755	8492	8665	8656
1.5	–	–	65	–	–	64	–	–	3297	–	–	–	8666
2	52	52	65	54	52	69	2850	3286	3379	6976	8576	8734	8731
3	58	59	68	61	61	73	3013	3431	3497	7145	8646	8750	8749
5	64	64	69	66	67	75	3131	3545	3591	7355	8723	8759	8759
7	66	66	70	68	70	75	3215	3610	3644	7382	8735	8775	8771
10	69	69	70	71	74	75	3271	3665	3688	7405	8739	8782	8773

For mouse, fugu and pig, we examined the relative performances of sequence and multiple alignment databases. The multiple alignment used consisted of baboon, cat, chicken, chimp, cow, dog, human, mouse, pig and rat. The sequence database consisted solely of the closest sequence in the alignment to the query, and the multiple alignment database consisted of the multiple alignment projected to remove columns gapped in the closest sequence. Columns labeled H present results using STANDARD with human as the database, C present results using STANDARD with cow as the database, S present results using STANDARD with the projected alignment as the database, and T present results using Typhon with the projected alignment as the database. The testing methodology was the same as that used for tests comparing sensitivity results on the full alignment. There were in total 10 678 HHAs that could potentially be identified for mouse, 848 for fugu and 11 094 for pig.