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And , as this question forms in my mind , I begin to reflect on the shaky foundations of art history . The principle of using the phylogenetic profile of a DNA cis-regulatory site to identify a DNA-binding protein was demonstrated in the case of the NrdR-box associated with ribonucleotide reductase genes ; leading to the identification of the NrdR-box binding protein [ 45 ] . SavonaroIan puritanism has made Botticelli renounce the physical beauty which he still thought appropriate to the blessed spirits in his Dante drawings . The FLAME algorithm has intrinsic advantages , such as the ability to capture non-linear relationships and non-globular clusters , the automated definition of the number of clusters , and the identification of cluster outliers , i.e. genes that are not assigned to any cluster . tRNA genes are indicated by the one-letter amino acid code ( Me , elongator methionine ; Mf , initiator methionine ) followed by the anticodon in parentheses . In this case , the possible loss of specificity would be strongly compensated by the increased sensitivity in the identification of functional links related to mammalian-specific gene modules . The match of any one protein from the reference genome to the phylogenetic profile becomes optimized for that protein by automatic selection of the most favorable BLAST E-value cutoff .