Table 1.

Sensitivity and specificity of exon detection from the P. falciparum genome

Method & params	P.f /P.g		P.f /P.k		P.f /P.v		P.f /P.y		P.k /All		Total Time (Mins)
	Sen. (%)	Spe. (%)	Sen. (%)	Spe. (%)	Sen. (%)	Spe. (%)	Sen. (%)	Spe. (%)	Sen. (%)	Spe. (%)
XMAligner -hashSize = 20 -binaryHash = true -limit = 500
r = 0.15	76.44	75.94	57.61	83.53	55.94	86.21	75.81	81.49	80.12	79.71	451.62
r = 0.25	51.83	86.50	42.03	90.81	39.60	91.65	52.22	89.45	59.73	88.63	441.40
r = 0.35	35.37	93.55	31.13	94.54	28.76	94.58	36.11	93.92	44.08	93.31	439.53
Promer -l 6 -g 30
c = 10	78.43	50.48	66.88	51.13	62.66	51.61	80.37	51.80	87.55	52.85	327.21
c = 20	46.23	78.72	43.15	89.13	39.76	92.35	48.98	83.14	54.16	79.72	33.39
c = 40	34.38	86.36	29.83	95.92	27.13	97.32	32.92	90.01	31.14	87.89	28.23
Nucmer -l 14 -g 160
c = 40	18.94	73.82	6.64	52.99	3.61	41.80	17.54	74.50	22.12	72.79	17.76
c = 65	14.63	94.65	3.71	88.44	1.71	76.98	12.86	95.93	16.01	94.42	7.89
c = 90	11.69	97.10	2.22	87.52	0.86	73.31	10.08	97.33	12.20	96.65	6.66
Blastz -notransition -step = 20 -nogapped
t = 3000	34.24	75.35	19.26	69.03	13.74	73.91	30.96	82.19	44.97	75.65	34.57
t = 5000	28.16	95.56	15.51	93.58	11.43	94.55	25.82	96.43	37.89	94.78	31.23
t = 7000	24.73	96.88	14.05	96.02	10.69	95.88	23.43	97.03	33.31	96.35	30.89