I actually had a java program that did something very similar to this. It was very nice to just have the sequence as a string to read in, no parsing required! You can get the bare fasta formated sequence pretty easily if you use something like this: 

my $giNum  = 148261691
my $seq    = "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protei
+n&qty=1&c_start=1&list_uids="
.$giNum
."&uids=&dopt=fasta&dispmax=5&sendto=t&from=begin&to=end";

[download]


and then do something similar to what you're doing above.

good luck!

In reply to Re^2: Getting data from NCBI by jpearl
in thread Getting data from NCBI by Becky

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