A simplified schematic of ribosome profiling. Ribosome profiling begins with separating a cell’s polysomes (mRNA with ribosomes attached) from its lysate. Erosion by nuclease digestion removes all mRNA not shielded by a ribosome while also cleaving ribosomes
attached to the same mRNA strand. Subsequent removal of the ribosomes leaves behind
only the mRNA fragments which were undergoing translation at the point of cell lysis. Mapping these fragments back to the genome gives a codon-level resolution transcriptome-wide
overview of the translation occurring within the cell. From this we can infer the optimality
associated with any given codon from any given gene.