Escherichia Coli (E.coli)

Lisser and Margalit (1994) attempted to determine common structural features in Escherichia coli promoters with computer analysis. They studied four intrinsic sequence-dependent characteristics in Escherichia coli (E. coli) promoter regions: "helix stability, helix flexibility, and two conformational parameters represented by the DNA tendencies for B-Z and B-A transition" (p. 823). Quantitative measures for these properties were available for the ten dinucleotides from experimental or theoretical studies; these measures were summarized in Table 1. By summing the values of the dinucleotides along the sequence, a property value for a DNA segment was obtained (p. 824).

Helix stability was evaluated by "calculating the sequence-dependent free-energy values for helix to coil transition." DNA flexibility values, and B-Z and B-A transition tendencies, were determined by experimental and theoretical studies (p. 284).

The authors compiled a data set of E. coli promoter sequences to include 300 mRNA promoters whose transcriptional-start position had been defined experimentally. Redundant sequences were excluded; all promoter sequences were verified in the literature. Next, 300 non-promoter sequences were randomly selected from E. coli coding regions (p. 825).

Comparison between promoter and random sequences was evaluated by a t-test (p. 825). Discriminant analysis was done with the SPSS package and a computing program developed in Fortran 7

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