Amino Acid Dimers in S. cerevisiae
The actual abundance of amino acid dimers varied little from that predicted by the amino acid usage bias of the sequences. Figure 1 shows the actual and expected counts of all 400 amino acid dimers, which are arranged along the x-axis in order of increasing actual count.
Figure 2 shows the ratio scores for all nucleotide heptamers encoding the same a.a. dimers as the heptamers laboratory tested for frameshift efficiency (indicated in the figure legend.) Each line connects the ratio scores of the group of heptamers encoding a particular a.a. dimer. Because the heptamers in each group range in representation level, we conclude that the over- or underrepresentation of any heptamer is due primarily to selective forces acting on the nucleotide rather than amino acid sequence.
Note that many of the most overrepresented dimers are a.a. repeats; Figure 3 shows the ratio scores for all nucleotide heptamers encoding these repeats. Many of the encoding heptamers tend to be overrepresented as well, some far more than the encoded amino acid dimer.
