Figure 6

Codon clusters define specific codon-context rules in S. cerevisiae. (a) A major cluster of bad context is defined by codon pairs whose wobble base of the first codon is uridine (U) and the first base of the 3' neighbor is adenosine (A). This cluster defines a XXU-AYY context rule, in which X and Y are any nucleotide. Within this cluster some of the Asn and Ser codons represent exceptions to the above rule as their residual signal is positive (green cells). (b,c) Two of the good context clusters define two distinct codon context rules, namely (b) XXC-AYY and (c) XXU-GYY rules. As before, some of the codons within those clusters are exceptions to the above rules and a number of codons have no particular preferences or rejections (black cells).