When assigning the %amino_acid_conversion, you could use newlines to make the code a bit more readable

Completely agree. I'd go even further and put whitespace around the fat commas and with so many entries I would sort by either key or value to make it easier to spot misses/dupes/typos.

%amino_acid_conversion = (
    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'
);
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