Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins

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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Additional file 2:

The quadratic scaling of the total number of paralogous pairs with the number of genes in the genome. The total number of paralogous pairs ∑_pN_a(p) generated by the all-to-all alignment of all protein sequences encoded in the genome (the y-axis) scales as the square of the total number N_genes of protein-coding genes in the genome. Solid symbols are six model organisms used in our study. The solid line has the slope 2 on this log-log plot.

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