Fig. 2

Ribosome profiling reveals novel and annotated open reading frames. a Shown are examples of PASA-updated Toxoplasma transcript structure annotations (Black) and the corresponding current ToxoDB transcript annotation (Blue). A) The PASA-updated transcript is due to the addition of 5′/3′UTRs (red arrows). Prediction of ORFs based on the PASA-updated transcript structures in RiboTaper identified canonical and novel ORFs. The novel ORFs were mainly due to; b alternative splicing of annotated transcripts (skipped exon, red arrow), c potentially mis-annotated transcripts structures, and d novel transcripts. The RiboTaper-predicted ORFs in B-D are presented as red blocks. In all the figures, Ribo-seq and RNA-seq read coverage on each transcript is shown in Fragment per kilobase exon per million reads (FPKM)