Consensus patterns in DNA

Matrices can provide realistic representations of protein/DNA specificity. In many cases simple mononucleotide-based matrices are adequate representations, but more complex matrices may be needed for other cases. Unlike simple consensus sequences, matrices allow for different penalties to be assessed for different changes to a binding site, a property that is essential for accurate description of a binding site pattern. When only a collection of binding site sequences is known, the best representation for the pattern is an information content formulation, based on both thermodynamic and statistical considerations. Quantitative data on relative binding affinities may be used to determine matrices that provide a best fit to the data. Matrix representations also provide an efficient method of aligning multiple sequences to identify binding site patterns that they have in common.