This is called codon bias . Simply tabulating codon frequencies is one example of a coding measure, that is, a rule for calculating a number, or table of numbers, meant to summarize such regularities. Introns mostly start with GT and end with AG . Promoter Gene Promoter region is the binding site for RNA polymerase, which initiates the process of gene transcription. This region is 25-30 base pairs upstream of gene.
Promoters are usually small and present high variability.
HMMs are flexible enough to model them. So once the promoter is detected one could detect a gene down stream of the promoter. A protein must bind to the DNA before it can bend . There is a sequence for this bending in the DNA structure. This bending can create characteristic sites that may include hydrophobic and hydrophilic centers as well as others.