From your posts, it seems that you are working with genome sequences. I suggest you give BioPerl a try. It might be slower, but you'll be able to do a lot with very little coding.

In particular, they have a Bio::Seq::LargePrimarySeq module to deal with large sequences such as the ones that you are working with. Give it a go, it's funnier than reinventing wheels poorly.

In reply to Re: Lower-casing Substrings and Iterating Two Files together by bruno
in thread Lower-casing Substrings and Iterating Two Files together by neversaint

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