Figure 2

Empirical cDNA-AFLP data are highly structured. Patterning of cDNA-AFLP data. A and B: Patterning of complete arrays of selective PCR amplifications using CviAII and MseI restriction enzymes for (A) simulated random DNA, (B) simulated cDNA (following the standard eukaryotic codon table [25]), and (C) Homo sapiens cDNA. 10000 sequences of 1290 bp were simulated for both the DNA and cDNA datasets. Pixel intensity reflects the relative proportion of products obtained during selective in silico PCR. Pixels are ordered by selective base pairs: AAA (left, top) to TTT (bottom, right). White pixels indicate that no fragments were generated for this combination of selective base pairs.