Downloaded from genome. cshlp org on June 23, 2011-Published by Cold Spring Harbor Laboratory Press tzkovitz and Alon Val Ala D [ Figure 1. Alternative genetic codes. (A)The real code. (B)An alternative code obtained by an AeG permutation in the first position. (O An alternative ode obtained by an Ae)C permutation in the second position, and (D) AeG permutation in the third position. odons are marked in red start Met) codons in green. Codons that are changed relative to the real code are in gray. There are 4! x 4l x 2=1152 alternative codes obtained by mple,(B) the nine neighboring codons of the Valine codon marked with a red arrow in the real code(shown in A)are the same as(a) the nine eighboring codons of the Valine codon marked with a red arrow in the alternative code shown in B Solid lines connect codons differing in the first tter, dotted lines connect codons differing in the second letter, and dashed lines connect codons differing in the third letter. Different amino acids are displayed in different colors. This equivalence applies to all codons probability that this 5-mer appears in a coding region, one needs 5-mer cannot appear in a coding region in this frame, because 406 Genome researchNNU|GAC|ANN, or NUG|ACA, where N denotes any nucleotide and the vertical lines separate consecutive codons. To assess the probability that this 5-mer appears in a coding region, one needs to sum over the three possible reading frames (Fig. 2A). In one of the frames, this sequence generates a stop codon, UGA. The 5-mer cannot appear in a coding region in this frame, because Figure 1. Alternative genetic codes. (A) The real code. (B) An alternative code obtained by an A↔G permutation in the first position. (C) An alternative code obtained by an A↔C permutation in the second position, and (D) A↔G permutation in the third position. Stop codons are marked in red, start (Met) codons in green. Codons that are changed relative to the real code are in gray. There are 4!
4!
2 = 1152 alternative codes obtained by independent permutations of the nucleotides in each of the three codon positions. (E,F) Structural equivalence of real and alternative genetic codes. For example, (E) the nine neighboring codons of the Valine codon marked with a red arrow in the real code (shown in A) are the same as (F) the nine neighboring codons of the Valine codon marked with a red arrow in the alternative code shown in B. Solid lines connect codons differing in the first letter, dotted lines connect codons differing in the second letter, and dashed lines connect codons differing in the third letter. Different amino acids are displayed in different colors. This equivalence applies to all codons. Itzkovitz and Alon 406 Genome Research www.genome.org Downloaded from genome.cshlp.org on June 23, 2011 - Published by Cold Spring Harbor Laboratory Press