POFs are more likely to be species specific than PDFs. POFs are more likely to be species specific than PDFs among 10 different proteomes (S. cerevisiae, Sc; S. pombe, Sp; A. thaliana, At; O. sativa, Os; D. melanogaster, Dm; A. gambiae, Ag; M. musculus, Mm; R. norvegicus, Rn; H. sapiens, Hs; C. elegans, Ce). (a) Proportion of POFs and PDFs represented in unique protein sets determined among the 10 different proteomes. Specificity of a protein to a particular proteome was determined based on a BLAST e-value cutoff of 10-6. Numbers on top of bars donate the total number of proteins in each group. (b) Relationship trees among the 10 different proteomes shown in (a). Trees were constructed based on PDFs (dashed blue line) or POFs (red line). Proteome analyses, BLAST comparisons and tree construction were performed as described in Materials and methods. Outl., an outlier E.coli genome was used.