Just sneaking suspicion and wild surmise here, can't test this, but your command line is something like
    perl programName.pl mRNA.fa
and not
    perl <programName.pl> <mRNA.fa>
isn't it? (The  < > angle brackets are just metasyntactic delimiters. (Update: Well, as used by your instructor, they're just metasyntactic delimiters. On a command line, of course, they're re-direction operators — a very significant difference!))