If your code does not display the "Hydrophobic stretch found in:" message, then the input file could exist, but be empty. Or, the input file does not have a line beginning with >, then followed by a tab, then followed by VILMFWCA. Is there a tab? You could try: 
        if ($sequence =~ /(^>)\s*(VILMFWCA)/){

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Is this a job for http://www.bioperl.org/wiki/Main_Page?

See also: How do I compose an effective node title?

In reply to Re: Where am I going wrong? by toolic
in thread Where am I going wrong? by lairel

Title:
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