If you haven't already heard of the Bioperl site you should head on over there and see about already optimized and tested solutions for the type of task you are trying to accomplish. In particular (I am not a bio-person), you should look on Bioperl scripts page.

In reply to Re: Splitting string (regex) while keeping the separator? by Sinistral
in thread Splitting string (regex) while keeping the separator? by Cantello

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