Characterizing the Shine-Dalgarno Motif: Probability Matrices and Weight Matrices

Methods for identifying biologically significant k-mers by exhaustive evaluation (k ≤ 10) are applied to the pooled Upstream Regions (USR) of all 4289 E. coli ORFs. Instances of the ShineDalgarno (SD) site are readily identified using these methods. Using these motif instances as starting points, two motif representations and training methods, probability and weight matrices, are applied to characterize the complete SD motif. Despite using different representations and objective functions, both methods yield approximately the same motif characterization, providing evidence for the robustness of the result and the effectiveness of the methods. By these measures, about 1/4 of the ORFs have no better than random SD sites.