supriyoch 2008:

This is a commonly-asked question, so you should review the perlfaqX documents.

The typical solution is to store the sequences in a hash as you process them. So just before you process the sequence, check to see if it's in the hash. If so, skip to the next sequence. Then process the sequence and store it in the hash.

...roboticus

When your only tool is a hammer, all problems look like your thumb.