A database of nucleic acid sequences for germline-encoded CDR1 and 2 and frameworks 1, 2, and 3 of functional Ig V-regions was extracted from www.ncbi.nlm.nih.gov/projects/igblast and compiled as described (2). All available mouse and human V genes were used in the analyses. Framework regions (FRs) and CDR sequences were defined using the Kabat and/or IMGT definitions as indicated in the text or figure legends (20–22). The framework regions (FRs) 1–3 or CDR1 and 2 sequences were fused to form a continuous sequence, and codon frequencies were calculated by the function provided at http://www.kazusa.or.jp/codon/. This approach was made possible by the fact that CDR and FR definitions begin and end with intact codons. IgVH genes from cartilaginous fishes were extracted from http://www.imgt.org/. All 12 functional genomic DNA sequences available at the time of the analyses were used to determine the average observed/expected ratios of AGY and TCN Ser codons among germline-encoded CDRs. The following sequences were used in the analyses: Ginglymostoma cirratum (IGHV2S1*01, IGHV2S2*01, IGHV2S3*01, and IGHV2S4*01), Heterodontus francisci (IGHV1S1*01, IGHV1S15*01, IGHV1S3*01, IGHV1S4*01), Leucoraja erinacea (IGHV1S3*01, IGHV1S4*01, and IGHV1S5*01), and Hydrolagus colliei (IGHV1S3*01). Nucleotide sequences encoding mouse TCRV-region CDRs (IMGT definition) were also extracted from functional V genes at http://www.imgt.org/ (20). In cases where a V gene had multiple alleles, the first listed allele was analyzed.