Yes, you will want to read your sequence ID/positional data into an array, ideally an array of hashes were the hash keys would be something like "id", "start, "end".
Then you should probably use Bio::DB::Fasta to retrieve fragments of sequences from your FASTA file, but you could also use Bio::SeqIO and extract regions from your sequences using "substr" on the DNA string.

In reply to Re: extract sequence given positions from fasta by tospo
in thread extract sequence given positions from fasta by Gemchal

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