#!/usr/bin/perl -w
$proteinfilename = 'fragment.txt';
open(PROTEINFILE, $proteinfilename);
$protein = <PROTEINFILE>;
close PROTEINFILE;
print " here is the protein:\n\n";
print $protein;

##</code><code>##


readline() on closed filehandle PROTEINFILE at C:\strawberry\perl\bin\trial1.pl line 4
here is the protein:

Use of uninitialized value $protein in print at C:\strawberry\perl\bin\trial1.pl line 7