Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee

BMC Bioinformatics

Table 1 Comparison between the PSI-Coffee and other multiple sequence alignment methods on each BAliBASE2-ref7 family

family	MSAProbs	Kalign	PROMALS	MAFFT	ProbCons	PRALINE™	PSI-Coffee
SP
7TM	0.981	0.938	0.985	0.962	0.978	0.983	0.986
Nat	0.789	0.765	0.815	0.797	0.777	0.732	0.779
ACR	0.989	0.969	0.964	0.994	0.989	0.987	0.992
DTD	0.972	0.961	0.965	0.975	0.967	0.960	0.977
ION	0.817	0.810	0.761	0.788	0.862	0.837	0.783
MSL	0.965	0.936	1.000	0.980	0.958	0.986	0.971
PHOTO	0.957	0.928	0.954	0.949	0.957	0.965	0.955
PTGA	0.899	0.826	0.863	0.886	0.903	0.808	0.926
avg	0.921	0.892	0.913	0.916	0.924	0.907	0.921
Pairs	3,117,244	3,014,033	3,109,227	3,093,269	3,108,377	3,080,356	3,124,007
TC
7TM	0.600	0.360	0.690	0.440	0.550	0.560	0.620
Nat	0.190	0.190	0.100	0.110	0.180	0.180	0.250
ACR	0.830	0.620	0.530	0.890	0.830	0.810	0.880
DTD	0.540	0.580	0.400	0.540	0.520	0.580	0.620
ION	0.270	0.130	0.260	0.260	0.320	0.000	0.210
MSL	0.910	0.850	1.000	0.950	0.900	0.960	0.930
PHOTO	0.510	0.440	0.510	0.510	0.540	0.690	0.520
PTGA	0.400	0.320	0.280	0.370	0.400	0.270	0.400
avg	0.531	0.436	0.471	0.509	0.530	0.506	0.554
Cols	1,066	863	814	1,057	1,054	1,058	1,146

SP and TC are the accuracy figures reported by BAliScore 3.01 based on core regions (Additional file 1). The rows, Pairs and Cols, denote the sum of corrected aligned pairs and columns, respectively. The number of pairs and columns in the reference alignments are 3,294,102 and 1,781, respectively. The best performance of each family is marked in bold.

ISSN: 1471-2105