Additional file 1.

The overall shape of the PID histogram is independent of the alignment algorithm and the E-value cutoff. The PID histogram N_a(p) in the fly (D. melanogaster genomes when pairs of paralogous proteins were detected using the blastp algorithm [1] with E-value cutoff of 10^-10 (filled circles) and 10^-30 (open diamonds). The inset shows the ratio of these two histograms, which is very close to 1 for p > 40%. Thus the overall shape of N_a(p) in most of the Region II (Fig. 1) is nearly + cutoff independent. The N_a(p) also is insensitive to a particular algorithm used to align the pairs. Indeed, when paralogous pairs detected by the blastp with the E-value cutoff of 10^-10 (filled circles) were realigned using the Smith-Waterman algorithm [28] the resulting distribution (blue stars) changed very little.

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Axelsen et al. Biology Direct 2007 2:32   doi:10.1186/1745-6150-2-32