Wait ... you mean your proteins are not single letters? But actually a 9 digit number like 648040620
? Then the regex solution as mentioned above will not work and I think you better put your data in arrays and use List::Compare
to calculate the set intersection and such.
A program should be light and agile, its subroutines connected like a string of pearls. The spirit and intent of the program should be retained throughout. There should be neither too little or too much, neither needless loops nor useless variables, neither lack of structure nor overwhelming rigidity." - The Tao of Programming, 4.1 - Geoffrey James