Hi, your flat genbank files can be handled using the BioPerl suite. See this HowTo for a very detailed guide to IO, which includes genbank parsers (and a lot of others).

You'll be using the Bio::SeqIO module ( See Yes, even you can use CPAN for a guide on getting modules installed, or ignore if i am patronising you... ) to read in the files, test each sequence feature if it is in your region of interest, and if it is, write it out to a fresh (smaller) file. You can do all this on-the-fly, so your large file shouldn't trouble memory problems...

Have a read, have a go, and get back to the Monastery (with examples and code) if you are having problems. Hope this helps!

Update: Typos...

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