6.8 Local Sequence Alignment

log g i,j f(j) . For large n, the resulting PAM matrices often allow one to find related proteins even when there are practically no matches in the alignment. In this case, the underlying nucleotide sequences are so diverged that their comparison usually fails to find any statistically significant similarities. For example, the similarity between the cancer-causing ν-sis oncogene and the growth factor PDGF would probably have remained undetected had Russell Doolittle and colleagues not transformed the nucleotide sequences into amino acid sequences prior to performing the comparison.