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In contrast, in the case of O-PPSAM, the optimized training sequence embeds the pilot nucleos at the first and third positions of Ns' = 4 positions for nucleos.
The same test was also performed on the third positions of CGN codons.
The percentages of changes at the first, second and third positions of the codons were ∼26%, ∼11%, and ∼63%, respectively (Figure 2).
The small subunit protein rpsL is involved in decoding the second and third positions of the codon at the A-site of the ribosome.
Namely, CG1998 contain 6 exons, while CG11162 contains only 2. However, the last intron of both genes interrupts the coding sequence at very similar positions (i.e. between the second and the third positions of a Lys codon, Figure 3).
With Hsp70 HSEs excluded, overall HSEs vary among species (Tamura-Nei gamma distance: mean = 0.410, SE = 0.089; transversions only) as much as do the third positions of codons within the coding sequence of the genes in which they occur.
We used only the third positions of the codons.
Only the third positions of some codons may be fourfold degenerate.
Consequently, third positions of the CoI and CoII codons were removed in the following analyses.
Table 1 also presents the data for the third positions of codons only.
All model parameters were optimized independently for first, second, and third positions of codons.
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