If you're trying to get a unique seq of protein sequences from a PIR file, I'd suggest using a hash of arrays. Use the sequence as the key and store the accession number (or a hash or array of all attribs, or an object representing the record) in the array. 

$hash{$sequence} = [ $accnum1, $accnum2, ... ];

$hash{$sequence} = [
                        { ENTRY => ...
                          TITLE => ...
                          ORGANISM => ...
                          ACCESSIONS => ... },
                    ];

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If you don't need all of the other data in the record, you can use $hash{$sequence} = $count to track how many duplicates were observed.

Calling keys on the hash returns the unique set of sequences.

If there are a very large number of sequences in the input file, you might be better off using a database.

In reply to Re: how to remove duplicate strings? by bobf
in thread how to remove duplicate strings? by heidi

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