BMC Genomics 2005, 6:136 http://www.biomedcentral.com/1471-2164/6/136 TFhigeucroerr4elation between the hydrophobicity of a mitochondrial transcript and its pyrimidine content The correlation between the hydrophobicity of a mitochondrial transcript and its pyrimidine content. GRAVY scores were calculated using the ExPASy ProtParam website. Linear fit P-values were less than 0.001 for all panels. Linear fit R- values were (A) 0.82 (B) 0.75 (C) 0.90, and (D) 0.88. The numbers of membrane, soluble, and unknown protein-coding genes for the species in panels A-C are found in Table 1. proteins are soluble or membrane-bound. At high GRAVY scores there is a consistent excursion of membrane pro- teins from the correlation line. Also, the membrane pro- teins having low GRAVY scores and low pyrimidine content in the transcripts are likely peripheral membrane proteins. Interestingly, the strong correlation in Figure 4 also holds for Dictyostelium where almost all mitochon- drial transcripts are purine-rich. It has been noted that the hydrophobicity of a protein is related to the pyrimidine content of position 2 in the codons of the gene [11,12]. If this is the cause of the pat- tern that we see in the mitochondrial protein genes, then by splitting the DNA walk into three separate walks, one for each codon position, we would expect that the walk using codon position 2 would be responsible for the signal, while the walks for codon positions 1 and 3 might be random. Fig. 5 shows a pyrimidine-purine walk of each codon position of the human COX1 membrane protein transcript and the Chondrus crispus S12 soluble ribosomal protein transcript. For comparison, the pyrimidine-purine walk of the human 16S ribosomal RNA is also shown. The base composition of mitochondrial genome sections encoding rRNA and tRNA from other species is given in additional file 1: Table S1. These walks are given as exam- ples to show the uniformity of the signal along the length Page 7 of 12 (page number not for citation purposes)