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Table 2 Profile-profile comparison F-measure for clustered sequences

From: Evaluation and improvements of clustering algorithms for detecting remote homologous protein families

Family
  TransClust HiFix MCL SCPS
Dataset F-measure Clusters Precision Recall F-measure Clusters Precision Recall F-measure Clusters Precision Recall F-measure Clusters Precision Recall
A-10 0.741 1608 0.924 0.732 0.652 2590 0.648 0.916 0.693 783 0.730 0.653 -  
A-20 0.749 1773 0.912 0.760 0.685 3022 0.672 0.840 0.703 922 0.736 0.703 -  
A-30 0.750 2098 0.868 0.814 0.695 3147 0.678 0.899 0.707 1257 0.731 0.706 -  
A-50 0.751 2951 0.860 0.804 0.702 4534 0.702 0.900 0.709 1653 0.724 0.702 -  
A-70 0.753 3153 0.858 0.818 0.713 4673 0.709 0.909 0.712 1817 0.727 0.706 -  
A-90 0.767 2714 0.833 0.870 0.717 4708 0.889 0.710 0.715 1945 0.743 0.708 -  
A-95 0.769 2800 0.766 0.840 0.725 4725 0.709 0.907 0.743 2078 0.768 0.709 -  
GOLD 0.959 94 0.950 0.978 0.921 98 0.906 0.918 0.925 81 0.961 0.922 -  
Super-family
A-10 0.722 1455 0.997 0.623 0.699 1182 0.963 0.636 0.752 714 0.908 0.726 0.750 186 0.742 0.763
A-20 0.783 1402 0.990 0.720 0.701 1319 0.964 0.644 0.754 848 0.916 0.738 0.759 253 0.934 0.654
A-30 0.809 1676 0.988 0.757 0.705 1500 0.942 0.686 0.778 1062 0.920 0.774 0.777 453 0.914 0.618
A-50 0.827 1995 0.987 0.778 0.710 2375 0.964 0.702 0.781 1642 0.968 0.723 0.789 665 0.958 0.693
A-70 0.833 2120 0.988 0.783 0.711 2476 0.960 0.707 0.788 1585 0.936 0.782 0.792 758 0.983 0.703
A-90 0.835 2213 0.988 0.779 0.715 2524 0.950 0.701 0.805 1799 0.965 0.755 0.805 931 0.993 0.700
A-95 0.837 2293 0.989 0.777 0.716 2582 0.960 0.708 0.807 1806 0.948 0.795 0.805 1023 0.995 0.703
GOLD 0.999 6 1 0.999 0.974 7 1 0.953 1.000 5 1 1 1.000 5 1 1
  1. Number of clusters found, and weighted mean precision and recall values for each clustering algorithm are shown. Best values are shown in bold.
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BMC Bioinformatics

ISSN: 1471-2105

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