Lncident: A Tool for Rapid Identification of Long Noncoding RNAs Utilizing Sequence Intrinsic Composition and Open Reading Frame Information

Table 2

Comparisons of C. elegans.

Tools	Sensitivity	Specificity	Accuracy	-measure	MCC	Kappa
CPC.web	0.9990	0.9895	0.9942	0.9942	0.9885	0.9884
CPAT.web	0.9910	0.9187	0.9548	0.9564	0.9120	0.9097
CNCI	0.9938	0.7744	0.8841	0.8955	0.7873	0.7681
PLEK	0.9987	0.4526	0.7256	0.7845	0.5387	0.4513
Lncident	1	0.9545	0.9772	0.9778	0.9555	0.9545
CPAT.train	0.9995	0.9950	0.9972	0.9973	0.9945	0.9945
PLEK.train	0.9795	0.9950	0.9872	0.9872	0.9746	0.9745
Lncident.train	0.9950	0.9975	0.9962	0.9962	0.9925	0.9925

For tools with default models, Lncident presented the best result among the alignment-free methods. Both Lncident and CPAT outperformed CPC by utilizing new-trained model. with model trained on human. suffix of “train” means the tools with model trained on C. elegans.