Transcribed-strand asymmetries as a function of GC3.

<p>The sum within each GC-sorted gene group of the absolute values of the differences (deltas) between values for complementary bases, 3|1 dinucleotides, and trinucleotides (top, middle, and bottom). At the top left are overall base-occurrence asymmetries at each codon position and on the right the TvsA and CvsG individual deltas. Also shown are base-composition predictions for all genes and asymmetries in 90 ribosomal-protein genes (subdivided into 6 groups, white signs, left plot only). In the middle and bottom are occurrence asymmetries and motif-preference asymmetries (left, right), for 3|1 dinucleotides and for codons or across-codon trinucleotides (see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002145#pone-0002145-g016" target="_blank">Figure 16</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002145#pone-0002145-g017" target="_blank">17</a> for individual-motif deltas). Grey lines on the left are the base-composition expectations and on the right the “null” asymmetries of motif preferences from genes with previously randomized synonymous-codon locations. The +signs are for ribosomal-protein genes and the white +'s are the base-composition predictions.