>> load MT_CDC1551
I put all the genes together:
>> genes=genoma.gene.sec(:);
>> genes=genes(genes~=0);
Compute the probabilities of hidden stop codons between each pair of aminoacids:
>> load codigo_MycobTub
>> [probstop_fr1_gen,probstop_fr2_gen]=gen2probstop(genes,codigo);
>> subplot(1,2,1)
>> imagesc(probstop_fr1_gen)
>> colorbar
>> subplot(1,2,2)
>> imagesc(probstop_fr2_gen)
>> colorbar
>> sum(probstop_fr1_gen(:))
ans =
16.8621
>> sum(probstop_fr2_gen(:))
ans =
19.1280
I compare them with the theoretical ones:
>> [probstop_fr1,probstop_fr2]=paresaa2probs(codigo);
>> figure
>> subplot(1,2,1)
>> imagesc(probstop_fr1)
>> colorbar
>> subplot(1,2,2)
>> imagesc(probstop_fr2)
>> colorbar
>> sum(probstop_fr1(:))
ans =
18.7500
>> sum(probstop_fr2(:))
ans =
24.5000
So the probability in the genes is actually LOWER than expected. Puaj.
But now, I will take into account the codon bias:
>> codones=gen2codones(genes);
>> hist(codones,1:65)
(codon 65 are unidentifiable codons, due to an error in sequentiation)
>> probcodones=hist(codones,1:65);
>> probcodones=probcodones(1:64);
>> probcodones=probcodones/sum(probcodones);
>> [probstop_fr1,probstop_fr2]=paresaa2probs(codigo,probcodones);
>> close all
>> subplot(1,2,1)
>> imagesc(probstop_fr1)
>> colorbar
>> subplot(1,2,2)
>> imagesc(probstop_fr2)
>> colorbar
>> sum(probstop_fr1(:))
ans =
16.6937
>> sum(probstop_fr2(:))
ans =
18.4024
With the codon bias, the theoretical prediction is slightly lower than the experimental result, especially in the frame 2 (frame -1). Let us see the relative probability:
>> subplot(1,2,1)
>> imagesc(probstop_fr1_gen./probstop_fr1)
>> colorbar
>> subplot(1,2,2)
>> imagesc(probstop_fr2_gen./probstop_fr2)
>> colorbar
>> nanmean(nanmean(probstop_fr1_gen./probstop_fr1))
ans =
1.0142
>> nanmean(nanmean(probstop_fr2_gen./probstop_fr2))
ans =
1.0366
Psé.
16 June 2009 at 10:21 am
Un poco más de ánimo, que pinta bastante bien (por lo menos los colores son monos)
16 June 2009 at 10:26 am
¿notifican?