Thanks for all the help so far guys!
One last question: I have this code trying to capture the locus name and place it after the ">" but nothing I do lets me capture it. 
    while (<$in>) 
    {
        my $locus =~ /LOCUS\s+(\w+)/;           
        s/\^\^/>$locus\n^^\n/g;
        print $out $_;

    }

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within the file the Locus name is formatted like this
Created: Tuesday, July 12, 2005 4:14 PM
LOCUS       AJ877264                 704 bp    DNA     linear   INV 15
+-APR-2005

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In reply to Re^3: Writing to file... by perl_n00b
in thread Writing to file... by perl_n00b

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