Figure 2.

Representation of the CAI, calculated using the human mean codon usage as a reference set, in the DNA sequence that encodes HPV63 E2 and E4. Part A represents the reading frame that encodes E2. Part B represents the same HPV63 genome fragment that encodes E2, but in the reading frame +1, which contains E4. The grey line in B represents the fragment of HPV63 E4 homologous to the closely related HPV1 E4. The black line in B represents the stretch also annotated as HPV63 E4, but which lacks homology with HPV1 E4. Note that the initial E4 region from HPV63, which is not homologous to the HPV1 gene, has an extremely low CAI, which suggests a wrong annotation for the E4 gene in HPV63. This figure was obtained using the output of the calculation of CAI along a sequence of the CAIcal server, with a window length of 11 and a window step of 5.