Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition

Table 8 Comparison of predictive accuracy of our method and MitPred for both plant and nonplant proteins in the TargetP data set

Predictor	Location	Sensitivity	Specificity	MCC
Our method	plant mTP	0.9348	0.8958	0.8587
MitPred (SVM)	plant mTP	0.8234	0.8584	0.7418
MitPred (BLAST+SVM)	plant mTP	0.9429	0.8422	0.8158
MitPred (HMM+SVM)	plant mTP	0.8668	0.8484	0.7644
Our method	nonplant mTP	0.7547	0.8333	0.7626
MitPred (SVM)	nonplant mTP	0.8194	0.8863	0.8302
MitPred (BLAST+SVM)	nonplant mTP	0.9380	0.9355	0.9268
MitPred (HMM+SVM)	nonplant mTP	0.8571	0.9408	0.8830

Note: In our methods, parameters shown in Table 2 of the manuscript were used, but "posconstraint" and "negconstraint" were not specified for nonplant mTP. For MitPred, we used default parameters as follows. In SVM method, threshold was set as 0.5. E-value cutoff of BLAST+SVM method was 1e-4. E-value and SVM threshold for HMM based Pfam search+SVM method were 1e-5 and 0.5 respectively.

ISSN: 1471-2105