## Analysis of hidden stops, separating the three stop codons

IMPORTANT: I change the programs gen2probstop.m and paresaa2probs.m

>> [probstop,casosfavorables,casostotales]=gen2probstop(genes,codigo);

First stop codon:

subplot(1,2,1)
imagesc(probstop{1}(:,:,1))
colorbar
subplot(1,2,2)
imagesc(probstop{2}(:,:,1))
colorbar

Second:
subplot(1,2,1)
imagesc(probstop{1}(:,:,2))
colorbar
subplot(1,2,2)
imagesc(probstop{2}(:,:,2))
colorbar

Third:

>> subplot(1,2,1)
imagesc(probstop{1}(:,:,3))
colorbar
subplot(1,2,2)
imagesc(probstop{2}(:,:,3))
colorbar

Now I compare with the theoretical probabilities:

>> codones=gen2codones(genes);
>> probcodones=hist(codones,1:65);
>> probcodones=probcodones(1:64);
>> probcodones=probcodones/sum(probcodones);
>> probstop_teor=paresaa2probs(codigo,probcodones);

Codón uaa:
>> c=1;
subplot(1,2,1)
imagesc(probstop{1}(:,:,c)./probstop_teor{1}(:,:,c))
colorbar
subplot(1,2,2)
imagesc(probstop{2}(:,:,c)./probstop_teor{2}(:,:,c))
colorbar

Codón uga:

c=2;
subplot(1,2,1)
imagesc(probstop{1}(:,:,c)./probstop_teor{1}(:,:,c))
colorbar
subplot(1,2,2)
imagesc(probstop{2}(:,:,c)./probstop_teor{2}(:,:,c))
colorbar

Codón uag:

c=3;
subplot(1,2,1)
imagesc(probstop{1}(:,:,c)./probstop_teor{1}(:,:,c))
colorbar
subplot(1,2,2)
imagesc(probstop{2}(:,:,c)./probstop_teor{2}(:,:,c))
colorbar