Sigma: multiple alignment of weakly-conserved non-coding DNA sequence

Siddharthan, Rahul

doi:10.1186/1471-2105-7-143

BMC Bioinformatics

Table 2 More results on synthetic yeast-like data. Same as Table 1, except that the sequences have five embedded motifs (drawn from weight matrices that had 80% "polarisation"); this better mimics real data and also improves the performance of all programs.

From: Sigma: multiple alignment of weakly-conserved non-coding DNA sequence

		q = 0.35				q = 0.45				q = 0.55				q = 0.65
5 embedded WM's
N _s	Prog	N ₊	N _-	Sen	Er	N ₊	N _-	Sen	Er	N ₊	N _-	Sen	Er	N ₊	N _-	Sen	Er
3	sigma+	0	0	0.00	N/A	0	0	0.00	N/A	13266	0	0.44	0.00	29352	0	0.98	0.00
	sigma-	0	0	0.00	N/A	456	0	0.02	0.00	19028	0	0.63	0.00	29274	0	0.98	0.00
	dialign	78	0	0.03	0.00	60	0	0.02	0.00	2639	0	0.09	0.00	11383	40	0.38	0.00
	alignm	3067	506	0.10	0.14	11389	2153	0.38	0.16	24496	1217	0.82	0.05	28687	305	0.96	0.01
	clustalw	20814	9186	0.69	0.31	26730	3270	0.89	0.11	29341	659	0.98	0.02	29878	122	1.00	0.00
	mlagan	17160	12840	0.57	0.43	26930	3070	0.90	0.10	29716	284	0.99	0.01	30000	0	1.00	0.00
	tcoffee	10421	19579	0.35	0.65	20548	9452	0.68	0.32	28129	1871	0.94	0.06	29887	113	1.00	0.00
6	sigma+	0	0	0.00	N/A	1625	0	0.03	0.00	36055	28	0.60	0.00	58596	0	0.98	0.00
	sigma-	452	42	0.01	0.09	5984	0	0.10	0.00	47264	26	0.79	0.00	58876	0	0.98	0.00
	dialign	510	144	0.01	0.22	1719	74	0.03	0.04	10250	0	0.17	0.00	33979	0	0.57	0.00
	alignm	3893	181	0.06	0.04	28300	1363	0.47	0.05	54487	1077	0.91	0.02	59496	170	0.99	0.00
	clustalw	42116	17884	0.70	0.30	53797	6203	0.90	0.10	58316	1684	0.97	0.03	59613	387	0.99	0.01
	mlagan	29458	30542	0.49	0.51	53833	6167	0.90	0.10	59427	573	0.99	0.01	60000	0	1.00	0.00
	tcoffee	25878	34122	0.43	0.57	47767	12233	0.80	0.20	58708	1292	0.98	0.02	59975	25	1.00	0.00
9	sigma+	40	30	0.00	0.43	2300	0	0.03	0.00	56847	20	0.63	0.00	87436	0	0.97	0.00
	sigma-	322	30	0.00	0.09	5805	0	0.06	0.00	69821	120	0.78	0.00	88775	0	0.99	0.00
	dialign	450	80	0.01	0.15	2844	106	0.03	0.04	20179	0	0.22	0.00	59400	0	0.66	0.00
	alignm	10165	652	0.11	0.06	60374	2420	0.67	0.04	85011	933	0.94	0.01	89651	201	1.00	0.00
	clustalw	62461	27539	0.69	0.31	83233	6767	0.92	0.08	86738	3262	0.96	0.04	89167	833	0.99	0.01
	mlagan	33857	56143	0.38	0.62	81225	8775	0.90	0.10	88869	1131	0.99	0.01	90000	0	1.00	0.00
	tcoffee	43416	46584	0.48	0.52	76928	13072	0.85	0.15	89240	760	0.99	0.01	89990	10	1.00	0.00

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ISSN: 1471-2105

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