Table 2.

Test data set analysis.

		2+ SRRs			3+ SRRs
		Loose Repeat Threshold			Loose Repeat Threshold
Total Proteins	SRR Proteins	Total	True positives	False positives	Total	True positives	False positives
5000	250	342	250 (100%)	92	248	248 (99.2%)	0
5000	1250	1306	1250 (100%)	56	1237	1237 (99.0%)	0
10000	500	674	500 (100%)	174	492	492 (98.4%)	0
10000	2500	2633	2500 (100%)	133	2466	2466 (98.6%)	0
		Normal Repeat Threshold			Normal Repeat Threshold
Total Proteins	SRR Proteins	Total	True positives	False positives	Total	True positives	False positives
5000	250	256	250 (100%)	6	248	248 (99.2%)	0
5000	1250	1253	1248 (99.8%)	5	1237	1237 (99.0%)	0
10000	500	506	499 (99.8 %)	7	492	492 (98.4%)	0
10000	2500	2504	2496 (99.8%)	8	2466	2466 (98.6%)	0
		Strict Repeat Threshold			Strict Repeat Threshold
Total Proteins	SRR Proteins	Total	True positives	False positives	Total	True positives	False positives
5000	250	245	245 (98.0%)	0	244	244 (97.6%)	0
5000	1250	1220	1220 (97.6%)	0	1219	1219 (97.5%)	0
10000	500	485	485 (97.0%)	0	484	484 (96.8%)	0
10000	2500	2424	2424 (97.0%)	0	2420	2420 (96.8%)	0

Proteomes containing 5000 or 10000 proteins (5% or 25% of which contained repeat regions) were created and analysed using RepSeq.