MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts

Table 1 Total SP scores on the full-length BAliBASE 3.0 subsets.

MSA tools	RV11	RV12	RV20	RV30	RV40	RV50
MSACompro	73.14	94.84	93.30	87.16	92.11	91.41
Clustalw	50.06	86.44	85.16	69.76	78.93	74.24
DIALIGN-TX	51.52	89.18	87.87	73.64	83.64	82.28
FSA	50.28	92.38	86.7	66.27	85.87	78.21
MAFFT	55.13	88.82	89.33	79.08	87.55	84.69
MSAProbs	68.18	94.65	92.81	83.19	92.47	90.76
MUSCLE	57.16	91.54	88.91	78.24	86.49	83.52
Opal	66.18	93.70	90.39	80.18	76.25	87.36
POA	37.96	83.19	85.28	69.18	78.22	71.49
Probalign	69.51	94.64	92.57	82.03	92.19	88.86
ProbCons	66.97	94.12	91.67	81.28	90.34	89.41
T-coffee	66.77	94.08	91.61	80.57	89.96	89.43

Bold denotes the highest scores. MSACompro yielded the highest SP scores on all the subsets except RV40. On some datasets such as RV11 and RV30, the improvement is substantial.

ISSN: 1471-2105