Reanalysis of the probabilities of stop codons for each pair of aminoacids

PROBABILITIES IN THE GENES:

>> genes=genoma.gene.sec’;
>> genes=genes(genes~=0);
>> [probstop,casosfavorables,casostotales]=gen2probstop(genes,codigo);
>> subplot(1,2,1)
>> imagesc(sum(probstop{1}(:,:,:),3))
>> colorbar
>> subplot(1,2,2)
>> imagesc(sum(probstop{2}(:,:,:),3))
>> colorbar

THEORETICAL PROBABILITIES:

>> probcodones=hist(codones,1:65);
>> probcodones=probcodones(1:64);
>> probcodones=probcodones/sum(probcodones);
>> probstop_teor=paresaa2probs(codigo,probcodones);
>> clf
>> subplot(1,2,1)
>> imagesc(sum(probstop_teor{1}(:,:,:),3))
>> codones=gen2codones(genes);
>> colorbar
>> subplot(1,2,2)
>> imagesc(sum(probstop_teor{2}(:,:,:),3))
>> colorbar

RATIO:

>> subplot(1,2,1)
>> imagesc(sum(probstop{1}(:,:,:),3)./sum(probstop_teor{1}(:,:,:),3))
>> colorbar
>> subplot(1,2,2)
>> imagesc(sum(probstop{2}(:,:,:),3)./sum(probstop_teor{2}(:,:,:),3))
>> colorbar

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Catastrophe

All previous results about hidden codons are wrong. When I generate the vector with the complete genome I make

>> genes=genoma.gene.sec(:);
>> genes=genes(genes~=0);

The second instruction goes column-wise, so it is not taking the genes properly. Instead, it takes all first bases, then all second bases and so on.

Agh.

Note that some results were significant. We should check the reason for that…