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

BMC Bioinformatics

Table 4 Results on uncorrelated data. Performance of various multiple sequence alignment programs on synthetic data with no dinucleotide correlations, and each base having probability 0.25. See the caption of Table 1 for explanation of the column and row labels.

		q = 0.35				q = 0.45				q = 0.55				q = 0.65
No 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	260	0	0.01	0.00	11690	0	0.39	0.00	29154	0	0.97	0.00
	dialign	0	60	0.00	1.00	80	0	0.03	0.00	1000	0	0.06	0.00	7566	0	0.25	0.00
	alignm	0	0	0.00	N/A	6682	605	0.22	0.08	23338	656	0.78	0.03	28466	283	0.95	0.01
	clustalw	16675	13325	0.56	0.44	26450	3550	0.88	0.12	29340	660	0.98	0.02	29828	172	0.99	0.01
	mlagan	11280	18720	0.38	0.62	26874	3126	0.90	0.10	29767	233	0.99	0.01	30000	0	1.00	0.00
	tcoffee	3443	26557	0.11	0.89	12475	17525	0.42	0.58	27836	2164	0.93	0.07	29810	190	0.99	0.01
6	sigma-	0	0	0.00	N/A	0	0	0.00	N/A	23583	0	0.39	0.00	58986	0	0.98	0.00
	dialign	0	0	0.00	N/A	138	0	0.01	0.00	4588	0	0.08	0.00	28177	0	0.47	0.00
	alignm	0	0	0.00	N/A	13090	174	0.22	0.01	53252	824	0.89	0.02	59529	139	0.99	0.00
	clustalw	37040	22960	0.62	0.38	53438	6562	0.89	0.11	58432	1568	0.97	0.03	59727	273	1.00	0.00
	mlagan	15987	44013	0.27	0.73	50702	9298	0.85	0.15	58621	1379	0.98	0.02	59917	83	1.00	0.00
	tcoffee	13439	46561	0.22	0.78	35387	24613	0.59	0.41	58292	1708	0.97	0.03	59941	59	1.00	0.00

ISSN: 1471-2105