Fig. 3.

TOC distinguishes ORFs in 5′ leaders, CDSs and 3′ trailers. (A) A training set is constructed from RefSeq genes using (1) annotated CDSs (coding ORFs, blue) in the context of the whole transcript, (2) RPF-containing ORFs in the 5′ leader sequence (green) in the context of the 5′ leader, and (3) RPF-containing ORFs in the 3′ trailer (red) in the context of the 3′ trailer (see Materials and methods). The four metrics used to train the classifier are displayed in the gray box (TE, translational efficiency; IO, inside versus outside; FL, fragment length; DS, disengagement score). After training, TOC uses RPF-covered ORFs to classify transcripts. (B) The combination of the four metrics separates coding ORFs, leaders and trailers of the training set. Transcripts lacking a protein-coding ORF cluster with trailers and leaders of the training set, as shown for three validated zebrafish lncRNAs (black). The density of each measure is shown along the axes.