Observed over expected ratios were calculated by dividing the codon observed frequency (described above) by the expected frequency obtained from the codon use table for the species at http://www.kazusa.or.jp/codon/. Reading frame frequencies for CDR AGY triplets were determined manually, with the provision that any non-Ser AGY triplet that overlapped a FR–CDR boundary was conservatively included in the corresponding non-coding CDR Ser reading frame.