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<FORM ENCTYPE="multipart/form-data" ACTION="./foo.cgi" METHOD="POST">
Protease: <SELECT NAME="PARAM1">
...

<p> Please select a protein sequence file to upload: <BR> <INPUT TYPE=
+"FILE" NAME="SEQUENCE"> <p>
<INPUT TYPE="submit"> </FORM>

my $q = new CGI;

...
while (<$fh2>) {
...
}