Let’s start from where we left. Read the data from the file: mrna_seq.txt (to be found in the code snippets for this chapter). It contains the mRNA sequence we obtained previously (see Section 17.2).
Your task is to translate the language of nucleic acids to the language of proteins. To do that you will operate on triplets of nucleotide bases (also called codons). You start with the AUG triplet (the sequence starts with it) and replace it with a proper amino acid (proteins are build of amino acids like Strings are build of Chars), in this case it is methionine. Then you move to another triplet (there are no ‘commas’ in the genetic code) and assign the proper amino acid according to the standard genetic code. You finish the protein synthesis once you encounter a stop codon (UAA, UAG, UGA).
Since rewriting the Wikipedia’s table from the link above is mundane and boring, then I paste the genetic code below in Julia’s dictionary format.
# codon - triplet of nucleotide bases, aa - amino acid
codon2aa = Dict(
"UUU"=> "Phe", "UUC"=> "Phe", "UUA" => "Leu", "UUG" => "Leu",
"CUU" => "Leu", "CUC" => "Leu", "CUA" => "Leu", "CUG" => "Leu",
"AUU" => "Ile", "AUC" => "Ile", "AUA" => "Ile", "AUG" => "Met",
"GUU" => "Val", "GUC" => "Val", "GUA" => "Val", "GUG" => "Val",
"UCU" => "Ser", "UCC" => "Ser", "UCA" => "Ser", "UCG" => "Ser",
"CCU" => "Pro", "CCC" => "Pro", "CCA" => "Pro", "CCG" => "Pro",
"ACU" => "Thr", "ACC" => "Thr", "ACA" => "Thr", "ACG" => "Thr",
"GCU" => "Ala", "GCC" => "Ala", "GCA" => "Ala", "GCG" => "Ala",
"UAU" => "Tyr", "UAC" => "Tyr", "UAA" => "Stop", "UAG" => "Stop",
"CAU" => "His", "CAC" => "His", "CAA" => "Gln", "CAG" => "Gln",
"AAU" => "Asn", "AAC" => "Asn", "AAA" => "Lys", "AAG" => "Lys",
"GAU" => "Asp", "GAC" => "Asp", "GAA" => "Glu", "GAG" => "Glu",
"UGU" => "Cys", "UGC" => "Cys", "UGA" => "Stop", "UGG" => "Trp",
"CGU" => "Arg", "CGC" => "Arg", "CGA" => "Arg", "CGG" => "Arg",
"AGU" => "Ser", "AGC" => "Ser", "AGA" => "Arg", "AGG" => "Arg",
"GGU" => "Gly", "GGC" => "Gly", "GGA" => "Gly", "GGG" => "Gly"
)For convenience scientists often use one letter abbreviations of the amino acids as defined by IUPAC and displayed below.
# aa - amino acid,
# iupac - International Union of Pure and Applied Chemistry
aa2iupac = Dict(
"Ala" => "A", "Arg" => "R", "Asn" => "N", "Asp" => "D",
"Cys" => "C", "Gln" => "Q", "Glu" => "E", "Gly" => "G",
"His" => "H", "Ile" => "I", "Leu" => "L", "Lys" => "K",
"Met" => "M", "Phe" => "F", "Pro" => "P", "Ser" => "S",
"Thr" => "T", "Trp" => "W", "Tyr" => "Y", "Val" => "V",
"Stop" => "Stop"
)So as a final touch rewrite the amino acid sequence using the one-letter abbreviations above. As a result you should obtain the following sequence:
# AA - amino acids
expectedAAseq = "MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEAL" *
"YLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGA" *
"GSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN"