Automatic detection of anchor points for multiple sequence alignment

BMC Bioinformatics

Table 1 Sum-of-pairs score of ClustalW with anchor points on Balibase 3, compared to other usual aligners

Alignment	RV11	RV12	RV20	RV30	RV40	RV50
CLUSTALW 2.0	49.27	86.89	86.23	70.71	79.65	70.56
CW+pc. (2)	34.78	81.92	83.02	64.52	71.45	67.78
CW+pc. (6)	52.62	89.84	85.90	70.66	80.70	77.28
CW+pc. (12)	53.13	87.63	85.71	73.14	80.31	74.35
CW+c. pc. (2)	50.66	86.35	86.21	74.53	80.37	77.51
CW+c. pc. (6)	52.62	90.11	86.32	74.21	80.55	77.46
CW+c. pc. (12)	53.13	87.63	86.21	74.36	80.42	74.75
DIALIGN-TX	51.52	89.18	87.88	76.18	83.64	82.28
MAFFT 6.717b	66.19	93.36	92.72	87.08	92.19	90.25
MUSCLE 3.7	57.16	91.54	88.91	81.45	86.49	83.52
PROBCONS 1.12	66.97	94.12	91.68	84.53	90.34	89.41
T-COFFEE 7.81	66.77	94.08	91.62	83.81	89.96	89.43

This table gives the mean of the SP score on all data of each of the reference datasets of BAliBASE 3, for several multiple alignment schemes. CW+pc. (k) refers to the performance scores of ClustalW when supplied with the partial columns computed by MS4, for s_min = k; while CW+c. pc. (k) refers to the consistent partial columns for the same value.

ISSN: 1471-2105