Figure 3.

Prediction performance of incRNA. (A) Comparison between the performance of incRNA and two previously published methods, Rfam/Infernal and RNAz. (B) Comparison between the performance of our method using all features, only expression data (tiling array and RNA-seq features), and sequence and structural features only (GC%, DNA conservation, RNA secondary structure, and protein conservation). (C) Comparison between the performance of our method using all features, and sequence and structural features in addition to only small RNA-seq, tiling array, or poly-A+ RNA-seq data. (D) Predicted ncRNA scores and CDS scores of annotated genomic elements (gold-standard set) assigned by our full model. All known ncRNA bins have ncRNA scores of at least P_high and all other genomic elements (bins) have ncRNA scores of, at most, P_low. (E) Unannotated bins with ncRNA scores of at least P_high form our high-confidence candidate ncRNA bins, while bins with ncRNA scores between P_low and P_high form our medium-confidence candidate ncRNA bins. All predictions are applied on the pairwise alignments of C. elegans and C. briggsae.