Fig. 2

Inferring canonical ORFs from ribo-seq data. A ORFeus takes in mapped ribo-seq data, genome annotations, and genome sequences and returns predicted ORFs calculated using an HMM. B A simple HMM to model canonical translation includes states corresponding to the 5’UTR and 3’UTR as well as nucleotide 1 (blue), 2 (red), and 3 (grey) of each start codon (diamonds), sense codon (circles), and stop codon (squares). All nonzero transition probabilities are denoted with arrows. A schematic representation of the emission probabilities for each state are plotted below the corresponding states. C A more complex HMM includes states for each individual start, stop, and sense codon sequence. Idealized ribo-seq density for a transcript that undergoes canonical translation of a single ORF is depicted below the model. The input relative ribo-seq density \(\rho _i^t\) and nucleotide sequence \(x_i^t\) at each position inform the output state path prediction