Table 1.

SVM Peformance in Distinguishing Real From Pseudo Exons

Flanks
Splice sites
US
DS
3′
5′
Exon body
ROC
Specificitya
CVb 0.609 0.484
+ - - - - 0.791 0.638
- + - - - 0.784 0.618
+ + - - - 0.855 0.695
- - + - - 0.823 0.672
- - - + - 0.837 0.698
- - + + - 0.907 0.777
+ + + + - 0.932 0.825
- - - - + 0.946 0.841
+ + - - + 0.984 0.956
- - + + + 0.987 0.964
+
+
+
+
+
0.991
0.976

Performances are indexed by ROC values and specificity. Each row is an SVM test. ROC values were measured in untouched sets of ∼2200 real and ∼2300 pseudo exons. The first five columns indicate the components used by SVM. US, upstream; DS, downstream; TP, true positive; FN, false negative; FP, false positive; SE, sensitivity; SP, specificity.

a Specificity = TP/(TP + FP) at a sensitivity (SE = TP/(TP + FN)) of 0.90

b The SVM classified on the basis of the acceptor and the donor consensus values