MDAT- Aligning multiple domain arrangements

BMC Bioinformatics

Table 1 Results of running 3 different methods on the BaliBase3 benchmarks

	Set	MDA	MDA (MSA)	Mafft	Clustal omega
	RV11	-	47.78	52.91	59.01
	RV12	-	83.61	89.30	90.60
	RV20	-	80.49	89.31	90.21
SP	RV30	-	67.42	82.50	86.24
	RV40	-	77.14	87.79	90.17
	RV50	-	65.65	84.90	86.20
	Total	-	71.78	81.36	84.00
	RV11	-	24.13	25.76	35.76
	RV12	-	65.02	74.93	78.86
	RV20	-	22.51	31.56	44.95
TC	RV30	-	19.03	42.47	57.50
	RV40	-	33.57	47.98	57.90
	RV50	-	18.56	49.62	53.25
	Total	-	33.09	45.82	55.44
Time (s)	Total	10.37	31.75	92.82	438.08

SP denotes the sum of pairs score, TC the column score. The running times of MDAT includes time for constructing the MDA but not the time for running the domain annotation. The MDAT row shows the time for constructing the MDA only, while MDAT (MSA) shows the time for calculating the MDA with subsequent MSA construction.

ISSN: 1471-2105