Table 1 |
|||||||||
|
Comparison of SYSTERS, TribeMCL and single linkage clustering (SLC) on Pfam and ENZYME data sets (J: Jaccard Coeffcient, SE: Sensitivity, SP: Specificity). The best result in each row is shown in bold face. For the single linkage clustering only the results of the "best" clustering are shown together with the corresponding cutoff E-value. In the case of Sensitivity/Specificity these values were choosen according to the intercept point of the two curves when plotting the values for all possible E-value cutoffs. All clustering procedures were applied to the non-redundant data set and redundant sequences were added to the cluster sets again to compare to the "true" cluster sets: a33,963,365 pairwise values of 283,113 non-redundant sequences used for clustering and 442,872 redundant sequences used in comparison; b1,582,948 pairwise values of 38,176 non-redundant sequences used for clustering and 84,405 redundant sequences used in comparison. |
|||||||||
|
SLC |
SYSTERS |
TribeMCL at Inflation |
|||||||
|
best |
at cutoff |
Superfam. |
Subclust. |
1.1 |
2 |
3 |
4 |
5 |
|
|
|
|||||||||
|
Pfama |
|||||||||
|
|
|||||||||
|
J |
0.19362 |
1e-53 |
0.15637 |
0.20815 |
--- |
--- |
--- |
--- |
--- |
|
SE |
0.26886 |
1e-49 |
0.55272 |
0.48302 |
--- |
--- |
--- |
--- |
--- |
|
SP |
0.26536 |
1e-49 |
0.17902 |
0.26781 |
--- |
--- |
--- |
--- |
--- |
|
|
|||||||||
|
ENZYMEb |
|||||||||
|
|
|||||||||
|
A.B.C.D |
|||||||||
|
|
|||||||||
|
J |
0.88760 |
1e-21 |
0.77445 |
0.89670 |
0.60390 |
0.60074 |
0.59990 |
0.59942 |
0.59778 |
|
SE |
0.92295 |
1e-08 |
0.92931 |
0.92297 |
0.61323 |
0.60328 |
0.60224 |
0.60164 |
0.59989 |
|
SP |
0.93616 |
1e-08 |
0.82294 |
0.96924 |
0.97543 |
0.99304 |
0.99357 |
0.99388 |
0.99416 |
|
|
|||||||||
|
A.B.C.? |
|||||||||
|
|
|||||||||
|
J |
0.71527 |
1e-15 |
0.65915 |
0.72410 |
0.48721 |
0.47900 |
0.47803 |
0.47746 |
0.47600 |
|
SE |
0.74985 |
1e-03 |
0.75320 |
0.73727 |
0.49099 |
0.47996 |
0.47895 |
0.47836 |
0.47688 |
|
SP |
0.80855 |
1e-03 |
0.84073 |
0.97592 |
0.98445 |
0.99586 |
0.99601 |
0.99608 |
0.99617 |
|
|
|||||||||
|
Krause et al. BMC Bioinformatics 2005 6:15 doi:10.1186/1471-2105-6-15 |
|||||||||
