% Universal motif that describes common features of helix 8
% of SRP RNA, in the language of Overbeeks pattern matcher.
% The helix consists of 3 pairings, one terminal loop, and
% two internal loops.
%
% Probably not the best way to make the motif. Problem is
% the motif ends up too loose in order to accomodate all
% observed little variations. A better way would be to use
% the weight matrix option. But harder to write.
%
r1={au,ua,gc,cg,gu,ug}   % allowed pairs
r2={au,ua,gc,cg,gu,ug,ag,ga}   % allowed pairs

p1=5...5          % first pairing, left
BNA 1...2         % first internal loop, left
p2=3...3          % second pairing, left
YNAGK[1,1,0]      % second internal loop, left
p3=3...3          % third pairing, left
G (YYYY | NR) A   % terminal loop
r1~p3             % third pairing, right
AGCAG[1,0,0]      % second internal loop, right
r2~p2[0,0,0]      % second pairing, right
2...3             % first internal loop, right
r1~p1[1,2,1]      % first pairing, right


% Bacteria SRP motif (4.5S without the Bacillus extension)
%
r3={au,ua,gc,cg,ug,gu}

%p1=
%p1=5...14               % Helix 5
%1...7                   %
%p2=5...5                %
%1...11                  %

p3=4...5                     % Helix 8
4...7                        %
p4=3...3                     %
nnagg                        %
p5=3...3                     %
ggaa[1,0,0]                  %
~p5[0,0,0]                   %
agcag[1,0,0]                 %
~p4[1,0,0]                   %
2...3                        %
r3~p3[1,0,0]                 %

%1...14
%((~p2[1,0,0] | ~p2[0,1,0]) | ~p2[0,0,1])
%1...6
%~p1[1,0,0]


% Bacteria SRP motif (stringent)
%
r1={au,ua,gc,cg,ug,gu}
p1=4...5                
4...7                     
p2=3...3                   
nnagg                        
p3=3...3                     
ggaa[1,0,0]                  
r1~p3[0,0,0]                   
agcag[1,0,0]                 
r1~p2[1,0,0]                   
2...3                        
r1~p1[1,0,0]