in reply to NCBI sequence fetching
Instead of Bioperl you can try NCBI's eutils. In particular the EFetch tool to retrieve fasta sequences given a list of accession identifiers
In the eutils help page you can find a sample Perl program that you can download and execute locally. Try to understand what it does, and then try to modify it to fits your purposes.
If you have any problem in the process, do not hesitate to post a new question here
Hope this helps
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