Third Step "Translation"

In this phase each triplets of nucleotid form a codon and indicate a START,END,or simply an aminoacid

We will first create a list named "Codons" where we will form the triplets from our ARNm so we have:

• for i in range(0,len(ADN_5),3):
• Codons.append (ARNm[i]+ARNm[i+1]+ARNm[i+2])

we will walk the ADN_5 by a 3 steps each time,and the Codons list recive the three nucleotide ARNm[i]+ARNm[i+1]+ARNm[i+2] forming a triplet
Well this is now the most fastidious part of the programming typing ;)
This is the result in the Pytho shell:

We have now our Codons list and ready to translate each of them to a START,END,or an aminoacid working should follow this rule table according to the combination of the the triplet:

Ala   GCU GCC GCA GCG
Arg  CGU CGC CGA CGG AGA AGG
Asn  AAU AAC
Asp  GAU GAC
Cys  UGU UGC
Gln   CAA CAG
Glu   GAA GAG
Gly  GGU GGC GGA GGG
His  CAU CAC
Ile    AUU AUC AUA
Leu  CUU CUC CUA CUG UUA UUG
Lys  AAA AAG
Met/START AUG
Phe  UUU UUC
Pro  CCU CCC CCA CCG
Ser  UCU UCC UCA UCG AGU AGC
Thr  ACU ACC ACA ACG
Trp  UGG
Typ  UAU UAC
Val  GUU GUC GUA GUG
Met  AUG
Stopcodons UAA UAG UGA

First we will walk througth codons list to translate codons (Met/START AUG) , (STOP UGA UAG UAA) or other codon in this exp we look for the (Phe UUU UUC) and the (Met AUG)

• for i in range(len(Codons)):
• if Codons[i]=="AUG":
• Met_nb=Met_nb + 1
• for i in range(i,len(Codons)):
• if Codons[i]=="UUU" or Codons[i]=="UUC":
• display( "----------->Phe")
• Protide.append("Phe")
• Phe_nb=Phe_nb + 1
• if Codons[i]=="AUG":
• display( "----------->Met")
• Protide.append("Met")
• if Codons[i]=="UGA" or Codons[i]=="UAG" or Codons[i]=="UAA":
• display( "Traduction Stopped")
• Protide.append("STOP")
• STOP_nb=STOP_nb + 1

This is a part of the result in the Pytho Shell:

We created Counter's variables like Met_nb for the Met numbers,Phe_nb for the Phe numbers wich they increment each time we found a codon that much,like that we know the number of each aminoacid generated by this DNA sequence.

In the next Code fragment we will look for functionnel protides wich are those who begin with (Met/START AUG) and end with (STOP UGA UAG UAA) each time we found the START followed by the STOP codon we add to All_Protide list the whole fragment betwin STARTand STOP:

• for i in range(len(Protide)):
• if Protide[i]=="Met":
• j=i+1
• for j in range(len(Protide)):
• if Protide[j]=="STOP":
• All_Protide.append(Protide[i:j])
• break
• else:
• pass

 
  Python Shell result:

  Until this point we got our All_Protide list filled by the functionnel protides,the next step is to do some basic statistc graph to have a quantitative represention of this DNA fragment in term of nucleotid and aminoacid frequency.