Codon-Optimisation

Background:the goal is to introduce targeted mutations ina protein by using expanded genetic code, where a mixture of bases is present at a certain position. For example, codon ATB where B is a mixture of C, G and T encodes for both Ileand Met. One can incorporate such codons in a synthesized gene or oligo to get a low-complexity library. We want to modify all positions independently from each other.Unfortunately, some expanded tripletscode for more amino acids than necessary. Say, we want an amino acid to be either Ala, Ile or Val –there are many degeneratecodons that can encode for all three of them. For example,RYA (R = A or G, Y = C or T), however the same codon will also encode for Thr. There are additional possibilities, such as RYT or RYC, however they will again encode for Thr.Let’s define “codon efficiency” as the number of codons translated into desired amino acids divided by the total number of all codons encoded by the degenerate codon. E.g. RYA = (ACA, ATA, GCA, GTA), i.e. 4 total. ACA is Thr, ATA is Ile,GCA is Ala and GTA is Val.If Ile, Ala and Val are desired and Thr is not, thentheefficiency is 3/4 = 75%.Turns out that other possibilities such as RYT, RYC and a few others have the same 75% efficiency, we can use any of them. In the real life the choice would be driven by codon usage frequency in the target organism (yeast), but this is outside of the scope of this assignment.Task:1)Write a function that takes a setof amino acids (say, {‘A’,’V’,’I’}) and returns the setof most efficient codons and the achieved efficiencya.For {A’,’V’,’I’}the answer would be({'RYA', 'RYH', 'RYC', 'RYW', 'RYM', 'RYY', 'RYT'}, 0.75)2)Write a function that takes a setof amino acids and:a.if they can be encoded by codonswith 100% efficiency, returns theinputsetb.if they cannot be encoded by a codon with 100% efficiency, removes the minimal number of amino acids from the list such as the resulting list can be encoded with 100% efficiency. If there are multiple possibilities, return all of them.I.e. from {‘A’,’V’}one would get {‘A’,‘V’}since they can be both encoded by the a number of codons with 100% efficiency (say, GYT)From {‘A’,’I’,’V’}one would get {‘I’,’V’} and{‘A’,’V’} (both 100% efficient), but not {‘A’,’I’} since {‘A’,’I’} is only 50% efficient.Things to consider:1)Write everything in Python2 or 3, make use of standard libraries such as collections and itertools. To save time, we’re providing a Python file with genetic code already typed in2)In part (1), how do you want to handle situations when the resulting codon also encodes for stop?No single right answer here. 3)Assume that this function will be called >100 times from a parent routine. Think about precomputing or caching things, i.e. some of the results you computed for position 1 might be reused incalculating things for position 2