The Domain Theory (for recognizing promoters):

   % Promoters have a region where a protein (RNA polymerase) must make contact
   % and the helical DNA sequence must have a valid conformation so that
   % the two pieces of the contact region spatially align.
   % Prolog notation is used.
    promoter :- contact, conformation.

   % There are two regions "upstream" from the beginning of the gene
   % at which the RNA polymerase makes contact.
    contact  :- minus_35, minus_10.

   % The following rules describe the compositions of possible contact regions.
   minus_35 :- p-37=c, p-36=t, p-35=t, p-34=g, p-33=a, p-32=c.
   minus_35 :-         p-36=t, p-35=t, p-34=g,         p-32=c, p-31=a.
   minus_35 :-         p-36=t, p-35=t, p-34=g, p-33=a, p-32=c, p-31=a.
   minus_35 :-         p-36=t, p-35=t, p-34=g, p-33=a, p-32=c.

   minus_10 :- p-14 t, p-13 a, p-12=t, p-11=a, p-10=a, p-9=t. 
   minus_10 :-         p-13 t, p-12=a,         p-10=a,        p-8=t.
   minus_10 :-         p-13 t, p-12=a, p-11=t, p-10=a, p-9=a, p-8=t.
   minus_10 :-                 p-12=t, p-11=a,                       p-7=t.

   % The following rules describe sequence characteristics that produce
   % acceptable conformations.
   conformation :- p-47=c, p-46=a, p-45=a, p-43=t, p-42=t, p-40=a, p-39=c,
                   p-22=g, p-18=t, p-16=c, p-8=g,  p-7=c,  p-6=g,  p-5=c,
                   p-4=c,  p-2=c,  p-1=c. 
   conformation :- p-45=a, p-44=a, p-41=a.
   conformation :- p-49=a, p-44=t, p-27=t, p-22=a, p-18=t, p-16=t, p-15=g, 
                   p-1=a. 
   conformation :- p-45=a, p-41=a, p-28=t, p-27=t, p-23=t, p-21=a, p-20=a,
	           p-17=t, p-15=t, p-4=t.

   % If exact matches are required, this domain theory matches NONE
   % of the examples below.  Also note that some of the MINUS_35 rules
   % are subsumed by another MINUS_35 rule.  This occurs because the
   % biological evidence is inconclusive wrt the correct specificity.