Permutations of 4 amino acid sequence oligopeptide

Question

I have an assignment for a project to build a tetrapeptides library to screen against some target enzymes in silicon.

I am looking for a script to construct about 160000 tetrapeptide from the 20Amino acids permutations.

I am quite familiar with Bash, but am struggling to get a function to working.

Answer 1

The Python solution is here. IMO Bash definitely isn't a good solution for this calculation.

from itertools import permutations, combinations

one2all ={'A': ('A', 'ALA', 'alanine'),
          'R': ('R', 'ARG', 'arginine'),
          'N': ('N', 'ASN', 'asparagine'),
          'D': ('D', 'ASP', 'aspartic acid'),
          'C': ('C', 'CYS', 'cysteine'),
          'Q': ('Q', 'GLN', 'glutamine'),
          'E': ('E', 'GLU', 'glutamic acid'),
          'G': ('G', 'GLY', 'glycine'),
          'H': ('H', 'HIS', 'histidine'),
          'I': ('I', 'ILE', 'isoleucine'),
          'L': ('L', 'LEU', 'leucine'),
          'K': ('K', 'LYS', 'lysine'),
          'M': ('M', 'MET', 'methionine'),
          'F': ('F', 'PHE', 'phenylalanine'),
          'P': ('P', 'PRO', 'proline'),
          'S': ('S', 'SER', 'serine'),
          'T': ('T', 'THR', 'threonine'),
          'W': ('W', 'TRP', 'tryptophan'),
          'Y': ('Y', 'TYR', 'tyrosine'),
          'V': ('V', 'VAL', 'valine'),
          'X': ('X', 'GLX', 'glutaminx'),
          'Z': ('Z', 'GLI', 'glycine'),
          'J': ('J', 'NLE', 'norleucine'),
          'U': ('U', 'CYC', 'cysteinc')}
myprotein = [x for x in one2all.keys()]        
tetrapeps = combinations(myprotein,4)
peptide = []
count = 0
for x in list(tetrapeps):
    peptide.append(''.join(x))
for tetra in peptide:    
    permpeptides = list(permutations (tetra))
    for i in permpeptides:
        count +=1
        print (''.join(i))

I get 255024 permutations so more than the estimate of 160000, however the code is correct (please see Validation below).

Truncated output

.... JUXV UVXJ UVJX UXVJ UXJV UJVX UJXV VZJU VZUJ VJZU VJUZ VUZJ VUJZ ZVJU ZVUJ ZJVU ZJUV ZUVJ ZUJV JVZU JVUZ JZVU JZUV JUVZ JUZV UVZJ UVJZ UZVJ UZJV UJVZ UJZV XZJU XZUJ XJZU XJUZ XUZJ XUJZ ZXJU ZXUJ ZJXU ZJUX ZUXJ ZUJX JXZU JXUZ JZXU JZUX JUXZ JUZX UXZJ UXJZ UZXJ UZJX UJXZ UJZX

I cut and paste the amino dictionary from here (I wasn't going to write it by hand), AminoAcid.py by Pasteur.

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Validation

The theoretical number of permutations from 4 samples of 20 amino acids is

116280

However, the amino acid chart I used comprised 24 amino acids (I just copied and pasted it). The theoretical number for 24 amino acids is therefore:

255024

This was the number observed in the output of the above code and validated the calculation.

A permutations calutation can be performed online here

I am not sure how the expected output of 160000 was derived but suspect it was a guess.

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The permutation equation is as follows, the output of this equation and the code above coincide,

$$ P_{n, r}=\frac{n !}{(n-r) !}$$

n = no. amino acids

r = size of oligopeptide

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Permutation by repetition

If the permutation by repetition equation is sought (comment below). The code is:

from itertools import product
myprotein = [x for x in one2all.keys()]
print(len([p for p in product(myprotein, repeat=4)]))

for 20 amino acids this is:

160000

for 24 amino acids:

331776

Answer 2

Here's a bash solution using brace expansion and the single-letter codes for the 20 common amino acids:

aalist=D,E,K,R,H,N,Q,S,T,P,G,A,V,I,L,M,C,F,Y,W
eval printf '"%s\n"' {"$aalist"}{"$aalist"}{"$aalist"}{"$aalist"}

This prints 160,000 lines, one for each tetrapeptide.