By Shinji Ido
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55 Coding Regions measure the asymmetry in the distribution of each base among the three codon positions. With A = number of As in positions 1,4,7,10, . . A = number of As in positions 2,5,8,11, . . A = number of As in positions 3,6,9,12, . . 5) and similarly for G^C^, and Γ . The other four parameters are simply the frequencies of the four bases in the sequence: f f ,f , and f . 1. 1.
Since no rules for picking acceptable 5' - 3' junction pairs are given, this method appears to be of rather limited value when used alone. Possibly, inclusion of a search for the lariat branch point consensus might to some extent relieve this shortcoming, since the 3' splice almost invariably involves the first A G found in a rather narrow distance range downstream from the lariat loop. Taking a more eclectic approach, Nakata et al. (1985) include information not only from the 5' and 3' consensus patterns, but also from the estimated free energy of s n R N A - R N A base pairing and from known statistical differences between the nucleotide sequences of coding and noncoding regions in their prediction scheme.
As an example of this, organisms with a high G C content in their genome have a high percentage of G and C in the third-codon position; the other two positions, which are much more constrained by the amino acid sequence, differ much less in G C content between GC-rich and GC-poor organisms (Bernardi and Bernardi, 1985; Wada and Suyama, 1985; Bibb et al, 1984; Aota and Ikemura, 1986). A strong correlation between codon usage and t R N A content is also observed in many organisms (Ikemura, 1981a,b, 1985; Bulmer, 1987).