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aicda.m
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aicda.m
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%% download AICDA sequence
AICDA=getgenpept('Q9GZX7')
AICDA.Sequence
%% in silico trypsin digestion of AICDA with Trypsin
[AICDApartsT, AICDAsitesT, AICDAlengthsT] = cleave(AICDA, 'trypsin','missedsites',1)
plot(AICDAlengthsT)
hist(AICDAlengthsT)
size(AICDAlengthsT)
%% add PO3 to S/T/Y and calculate+write molecular weight of fragments to file
po3mm=MolMass('HPO3')
fileID = fopen('AICDAfragsT.tab.txt','w');
for i=1:size(AICDAsitesT,1)
if(AICDAlengthsT(i)>=8)
stypos=regexp(upper(AICDApartsT{i}),'[STY]')
fprintf(fileID,'%s\t%s\t%5.5f\n',[int2str(i),' ',int2str(AICDAlengthsT(i))], ...
AICDApartsT{i}, molweight(AICDApartsT{i}));
for j=1:size((stypos'),1)
fprintf(fileID,'%s\t%s\t%5.5f\n',[int2str(i),' ',int2str(stypos(j))], ...
AICDApartsT{i}(1:stypos(j)), molweight(AICDApartsT{i})+j*po3mm);
end
end
end
fclose(fileID);
%% in silico trypsin digestion of AICDA with http://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#LysC
[AICDApartsL, AICDAsitesL, AICDAlengthsL] = cleave(AICDA, 'lysc','missedsites',1)
plot(AICDAlengthsL)
hist(AICDAlengthsL)
size(AICDAlengthsL)
%% add PO3 to S/T/Y and calculate+write molecular weight of fragments to file
po3mm=MolMass('HPO3')
fileID = fopen('AICDAfragsL.tab.txt','w');
for i=1:size(AICDAsitesL,1)
if(AICDAlengthsL(i)>=8)
stypos=regexp(upper(AICDApartsL{i}),'[STY]')
fprintf(fileID,'%s\t%s\t%5.5f\n',[int2str(i),' ',int2str(AICDAlengthsL(i))], ...
AICDApartsL{i}, molweight(AICDApartsL{i}));
for j=1:size((stypos'),1)
fprintf(fileID,'%s\t%s\t%5.5f\n',[int2str(i),' ',int2str(stypos(j))], ...
AICDApartsL{i}(1:stypos(j)), molweight(AICDApartsL{i})+j*po3mm);
end
end
end
fclose(fileID);
%% in silico trypsin digestion of AICDA with ARG-C proteinase http://www.mathworks.se/help/bioinfo/ref/cleavelookup.html#brp475t-5
[AICDApartsA, AICDAsitesA, AICDAlengthsA] = cleave(AICDA, 'arg-c','missedsites',1)
plot(AICDAlengthsA)
hist(AICDAlengthsA)
size(AICDAlengthsA)
%% add PO3 to S/T/Y and calculate+write molecular weight of fragments to file
po3mm=MolMass('HPO3')
fileID = fopen('AICDAfragsA.tab.txt','w');
for i=1:size(AICDAsitesA,1)
if(AICDAlengthsA(i)>=8)
stypos=regexp(upper(AICDApartsA{i}),'[STY]')
fprintf(fileID,'%s\t%s\t%5.5f\n',[int2str(i),' ',int2str(AICDAlengthsA(i))], ...
AICDApartsA{i}, molweight(AICDApartsA{i}));
for j=1:size((stypos'),1)
fprintf(fileID,'%s\t%s\t%5.5f\n',[int2str(i),' ',int2str(stypos(j))], ...
AICDApartsA{i}(1:stypos(j)), molweight(AICDApartsA{i})+j*po3mm);
end
end
end
fclose(fileID);