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

BMC Bioinformatics

Table 3 Results on synthetic plasmodium-like data. Performance of various multiple sequence alignment programs on synthetic data generated with dinucleotide correlations that mimic the Plasmodium falciparum genome. 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	0	0	0.00	N/A	1036	0	0.03	0.00	24617	0	0.82	0.00
	sigma-	66	1070	0.00	0.94	9175	372	0.31	0.04	27959	0	0.93	0.00	29547	0	0.98	0.00
	dialign	292	1471	0.01	0.83	800	1582	0.03	0.66	4185	929	0.14	0.18	14957	104	0.50	0.01
	alignm	753	1563	0.03	0.67	5889	2085	0.20	0.26	20462	1846	0.68	0.08	27433	728	0.91	0.03
	clustalw	12057	17943	0.40	0.60	23528	6472	0.78	0.22	27965	2035	0.93	0.07	29814	186	0.99	0.01
	mlagan	7974	22026	0.27	0.73	21709	8291	0.72	0.28	29145	855	0.97	0.03	30000	0	1.00	0.00
	tcoffee	6865	23135	0.23	0.77	15398	14602	0.51	0.49	25261	4739	0.84	0.16	29043	957	0.97	0.03
6	sigma+	0	0	0.00	N/A	48	0	0.00	0.00	8033	0	0.13	0.00	54293	0	0.90	0.00
	sigma-	1684	8161	0.03	0.83	26675	4113	0.44	0.13	57619	86	0.96	0.00	59411	0	0.99	0.00
	dialign	294	7229	0.00	0.96	3423	5362	0.06	0.61	15806	2521	0.26	0.14	46203	75	0.77	0.00
	alignm	0	50	0.00	1.00	3678	237	0.06	0.06	42406	972	0.71	0.02	57938	610	0.97	0.01
	clustalw	26172	33828	0.44	0.56	46240	13760	0.77	0.23	55270	4730	0.92	0.08	59234	766	0.99	0.01
	mlagan	13737	46263	0.23	0.77	40430	19570	0.67	0.33	57668	2332	0.96	0.04	59931	69	1.00	0.00
	tcoffee	19149	40851	0.32	0.68	40764	19236	0.68	0.32	56346	3654	0.94	0.06	59532	468	0.99	0.01

ISSN: 1471-2105