Preparation of class about the genetic code

Replication of the calculation in HaigHurst91:

cd geneticcode

>> load codigo
>> MS0=NaN(10^5,1);
MS_bases=NaN(10^5,3);
for c=1:10^5
codigo_perm=permutacodigo(codigo);
[MS0(c),MS_bases(c,1:3)]=codigo2MS(codigo_perm.codon2aa,codigo.aa_prop(:,1));
if mod(c,10000)==0
fprintf(‘%g,’,c)
end
end
10000,20000,30000,40000,50000,60000,70000,80000,90000,100000,>>
>> [MS0_real,MS_bases_real]=codigo2MS(codigo.codon2aa,codigo.aa_prop(:,1));
>> hist(MS0,100)
>> hold on
>> ejes=axis;
>> plot(MS0_real*[1 1],ejes(3:4),’k’)

Global MS:

First base:

hist(MS_bases(:,1),100)
>> ejes=axis;
>> hold on
>> plot(MS_bases_real(1)*[1 1],ejes(3:4),’k’)

Second base:

hist(MS_bases(:,2),100)
ejes=axis;
hold on
plot(MS_bases_real(2)*[1 1],ejes(3:4),’k’)

Third base:

>> hist(MS_bases(:,3),100)
ejes=axis;
hold on
plot(MS_bases_real(3)*[1 1],ejes(3:4),’k’)

Proportion of single-point mutations that lead to synonymous codons (permutations do not maintain family boxes):

MS0_nobox=NaN(10^4,1);
MS_bases_nobox=NaN(10^4,3);
prop_syn=NaN(10^4,1);
for c=1:10^4
codigo_perm=permutacodigo_noboxes(codigo);
[MS0_nobox(c),MS_bases_nobox(c,1:3),prop_syn(c)]=codigo2MS(codigo_perm.codon2aa,codigo.aa_prop(:,1));
if mod(c,10000)==0
fprintf(‘%g,’,c)
end
end
hist(prop_syn,50)
hold on
ejes=axis;
plot(prop_syn_real*[1 1],ejes(3:4),’k’)
>> set(gca,’FontSize’,15)
>> xlabel(‘Proportion of synonymous single-point mutations’,’FontSize’,15)
>> ylabel(‘Number of cases’,’FontSize’,15)

One Response to “Preparation of class about the genetic code”

  1. gonzalopolavieja Says:

    Al,

    Maybe the open notebook is a good platform for the class. It might however, be better to have its own notebook and complete routines. That way they can copy all programs and try them out.

    BTW, look at PLoS Biol. First ref to the
    PNAS :)


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