Mapping proteins in the presence of paralogs using units of coevolution

BMC Bioinformatics

Table 1 The average recall and precision values in percent as well as the runtime in hours of TAG-TSEMA [8], TreeTop [10], MMM [9] and our method CUPID are shown.

	Recall	Precision	Runtime	#Instances
TAG-TSEMA [8]	56 %	45 %	730 h	488
TreeTop [10]	38 %	48 %	0.02 h	488
CUPID	56 %	50 %	30 h	488
MMM, a = 0.1 [9]	6 %	35 %	55 h	488
MMM, a = 0.2 [9]	15 % [61 %]	46 % [55 %]	121 h	394
MMM, a = 0.3 [9]	26 % [70 %]	57 % [64 %]	250 h	270
MMM, a = 0.4 [9]	35 % [71 %]	53 % [65 %]	323 h	214
MMM, a = 0.5 [9]	37 % [70 %]	44 % [65 %]	363 h	149

CUPID was terminated when either optimality was reached or a time limit of 5 minutes was hit; in the latter case, the best solution found until that time was used. TAG-TSEMA and TreeTop values are taken from [10]. MMM runs were subject to a time limit of 1 hour; the number of instances solved within this time limit are given in the last column. Precision and recall values are only determined for the set of solved instances. For the same set of solved instances the CUPID quality measure is given in square brackets.

ISSN: 1471-2105